Release Note
Agilent Genomic Workbench 6.0
Associated Products and Part Number
# G2566AA – Agilent Genomic Workbench with Feature Extraction provided as part of the Agilent
Scanner
# G4460AA - G4462AA - Agilent Genomic Workbench with Feature Extraction Commercial License
# G4463AA - G4465AA - Agilent Genomic Workbench with Feature Extraction Academic License
# G3794AA – G3799AA - DNA Analytics Software Modules
New functionalities in Agilent Genomic Workbench
The new release of Agilent Genomic Workbench, version 6.0 , offers many new functionalities:

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Agilent Genomic Workbench 6.0 combines databases for Feature Extraction (FE), eArrayXD,
Sample Manager, and DNA Analytics into one central database. Therefore, this version of the
Agilent Genomic Workbench supports custom microarray creation, image processing, sample
information management and analysis in a single flow, with the greatest level of data consistency
and ease of use. Microarray design information is created or retrieved once and used for all steps
within the process;
Agilent Genomic Workbench 6.0 supports server/client installation mode, which allows workgroup
level usage for concurrent data access, parallel software usage, and data sharing within the
organization;
Agilent Genomic Workbench 6.0 provides for the first time, eArray extended desktop (eArrayXD)
module, which supports custom microarray design and creation on your desktop without having to
upload data onto Agilent servers;
Agilent Genomic Workbench 6.0 provides for the first time, SureSelect Target Enrichment Quality
Analyzer, which allows quality assessments for SureSelect Target Enrichment experiments;
Agilent Genomic Workbench 6.0 automatically checks for software updates for all of its modules.
Agilent Genomic Workbench 6.0 offers new algorithms in analysis modules and also
improvements of existing analysis for ChIP, CGH and Methylation.
eArrayXD
eArrayXD is a new software module to the Agilent Genomic Workbench. eArrayXD provides you with the
same functionality that is found in the web-based version of eArray (http://earray.chem.agilent.com).
Features that are found in eArrayXD, but are not in web based eArray are:

Custom Genome Import for Genomic Tiling (CGH/ChIP/SureSelect)
With eArrayXD,you can upload a genome for any species, and create probes within the CGH and
ChIP application spaces, or baits within the SureSelect target enrichment space. This is
especially useful when your genome of interest is not supported by eArray web site.

Network Search
eArrayXD provides you with the ability to conduct searching for probe content and designing
probes via Gene Expression probe design tool or CGH/CHIP HD probe search tool using
CytoScape contextual search.

Array Visualizer
While designing the array, it is of much importance to the user if he can foresee how his array will
be finally laid out and if it will be beneficial in the current experiment. This feature will allow
viewing the array and its contents on UI along with probe’s locations on the array.
Features that are not supported in this release:

SureSelect Capture Array application space
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OLS application space
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Ordered layout in array design creation

Collaboration and Publish microarray design

Creation of microarray set

Filters on probe group/probe search results

Probe reannotation tool
Preloaded Data for eArrayXD:
Following data gets pre-populated with installation:
1.
2.
3.
4.
5.
6.
7.
8.
Annotation category – e.g. gene symbol, cytoband, accessions
Annotation sources – eg Ref, GeneBank, Unigene
Track data
Slide layouts – All public slide layouts
Control grids – All public and inactive control grids
eArray Parameters – Various eArray configuration parameters
Species – Species information for HD searches, Probe design, Probe score etc.
Installation information
Following data gets populated with data download:
Application Type
CGH
Array Designs/ Probe
Groups/ Probes
Array designs
Agilent Catalog data
All array designs with
Public Slide Layout/
Control Grid
Workgroup data
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
All workgroup array
designs with
‘Randomized’ feature
layout and status
‘Complete’ and
‘Submit’.
Designs which are
part of
Active/dissolved
collaboration are not
downloaded.
CGH
CGH
Probe Groups
Probes
All
None
ChIP/ CH3
Array design
All array designs with
Public Slide Layout/
Control Grid
All
All
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Expression
Probe Groups
Probes
All
None
Array design
All array designs with
Public Slide Layout/
Control Grid
All
All
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SureSelect Target
Enrichment
Probe Groups
Probes
All
All
Libraries
All
microRNA
All
All
Array design
All designs with Public
Slide Layout/ Control
Grid

All
All
All libraries with
status ‘Complete’ and
‘Submit’.
Libraries which are
part of
Active/dissolved
collaboration are not
downloaded.
All
All
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Probe Groups
Probes
All workgroup array
designs with
‘Randomized’ feature
layout and status
‘Complete’ and
‘Submit’.
Designs which are
part of
Active/dissolved
collaboration are not
downloaded.
All
All

Bait Groups
Baits
All workgroup array
designs with
‘Randomized’ feature
layout and status
‘Complete’ and
‘Submit’.
Designs which are
part of
Active/dissolved
collaboration are not
downloaded.
All designs with
status ‘Complete’ and
‘Submit’.
Designs which are
part of
Active/dissolved
collaboration are not
downloaded.
All
Not applicable
Misc.
Control Grids
All Public/InActive
Slide Layouts
All Public layouts
Limited control grids with
access to workgroup.
Agilent Genomic Workbench Core Utilities
The Agilent Genomic Workbench Core Utilities contained Sample Manager and Workflow Manager as
part of the 5.0 release. New to the 6.0 release is Feature Extraction 10.9 (FE), and the QC chart tool.
Specific additional functionality are:
Feature Extraction (FE) 10.9
The user has the choice to either launch Feature Extraction (FE) as a standalone executable, or as a
component of the Agilent Genomic Workbench. New features as part of the Agilent Genomic
Workbench 6.0 include:

One time retrieval of microarray design file (grid template) that supports eArrayXD, FE 10.9 and
DNA Analytics: while downloading an Agilent catalog design file or a design file that belongs to
your workgroup, FE 10.9 will initiate the download process and eArrayXD will complete the
database update to be ready for data analysis;
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Manually export custom protocols and metric sets from previous FE versions and import them in
FE 10.9;
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New stats (Report AF Hold, PMT Voltages, and Glass thickness) from tiff Header are included in
the text output file;
New FENoWindows commands are supported.
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Changes from last release include:
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QC chart tool is no longer installed with Feature Extraction software. QC chart functionalities are
provided through Agilent Genomic Workbench 6.0 QC Tool;
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QC chart is no longer generated after extraction completes;
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MSSQL database is no longer supported;
Array QC Tool
A replacement for the QC chart tool, the Array QC Tool is a Quality control reporting tool that helps
customer to assess microarray quality and analyze trends. Key functionality:
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Create new metrics and metric sets;
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Associate thresholds with metrics in a set;
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Import STATS and PARAMS from FE file;
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Create queries with different PARAMS or different conditions;
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Plot the trends from selected arrays; Export chart to PDF files;
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Export and import query results; import query results from previous versions of QC chart tool;
import and export metric sets.
Target Enrichment Quality Analyzer
In the 6.0 release, as part of the SureSelect Target Enrichment application space, you have access to
the Target Enrichment Quality Analyzer. The Quality Analyzer is used to characterize the
performance of a sequencing run in comparison with the targeted regions. Key features and
functionality:
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Generate QC reports with a set of standard metrics;
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Provides report on enrichment level for target intervals.
Sample Manager
The Sample Manager enables you to easily associate meta data (patient/sample information) with
individual microarray slides. The meta data is then persisted through the analysis process, making it
easier to follow trends and analyze data. Key functionality:
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Associate sample information (Array Naming)
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Enable sample information to show up in reports
Workflow Manager
The workflow manager enables you to automate and manage the data analysis process from a single
user interface. Using the Workflow Manager, you will be able to:
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Analyze Tiff, FE txt, UDF file or already loaded experiment;
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Create new analysis method or use a already created one;
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Filter out arrays using Metric Set filter created in QC module;
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Associate sample attributes loaded from sample manager;
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Create experiment at the end to view the results in the interactive mode;
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Create aberration report for each sample and save the result database;
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During a workflow run, support the ability of selecting a grid file; the ability to automatically
determine grid template the protocol; the ability to configure FE output file generation and output
location.
DNAAnalytics 6.0
Some key new featutres that are offered in this new release of DNAAnalytics 6.0

Ability to share analysis results
Creator of experiment can share experiment and experiment result to other users. Other users can then
view these results. Other entities are implicitly shared to all users with read permission and the owner
has full permissions on them.
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Batman Implementation
The Batman (Bayesian Tool for Methylation Analysis) implemented to be able to assign methylation calls
to probes in Methylation arrays.
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Cancel Undo functionality
Whenever an operation can be safely cancelled and system restored to a previous valid state, a “Cancel”
button is available in the corresponding progress bar. Upon clicking on this Cancel button, the system
goes back to the previous valid state. If such a valid state is not available and the operation cannot be
safely cancelled, the Cancel button is not available .
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CoC Lowess and variance stabilization
Lowess (LOcally WEighted polynomial regreSSion) algorithm normalizes the channels within each array
using a nonlinear polynomial fit to the data.
The variance stabilization method2 is an alternative to Lowess normalization that fits a regression curve
to signal intensities after applying an arcsinh(x) transform to each channel rather than a log(x) transform.
The arcsinh(x) transform attempts to adjust the variance so that it is more consistent across the range of
the data set.
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CoC visualization: option of Linear or log scale
With the current release, the data and results can now be visualized in both linear and Log scales. The
user has an option to configure and choose one or both of the scales.
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Handling of Non Unique Probes
In DNAx Analytics 5.0, the user had to specifically “expand” designs to be able to visualize or analyze non
unique probes. In the current release, all probes are imported by default. The non unique probes are
highlighted by a blue color in the table view and by a different symbol in the graphical view. The user can
choose to filter all or subset of non unique probes using Design level filters.
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Design level Filter
With this release, a new filter , namely Design filter is available. This filter can filter probes based on
homology, number of perfect match hits that a probe has , whether it is in a pseudoautosomal region, or
based on the performance score of the probe. This filter can be used to get various subset of probes (
including previous “unique, non expanded probes”).

Configurable colors and ranges for the views
In this release, users can choose the color schemes, what quantity to color by and different ranges which
should be displayed in different colors.

Create Tracks from Methylation Scores
Functionality of Creating tracks from methylation scores is added. In the earlier version (DNA Analytics
5.0), this functionality was available only for CGH scores.

Cytoband information display in Gene View
Displaying cytoband information in Gene View is added as an option.

Pre-defined Peak-shape Detection v2.0
This method uses the expected distribution of sheared DNA fragments to model the shape of increased
probe signal (“peaks”).
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Queries database
Ability to query database by executing three of the query types is added. The types are:
1. Aberration queries
2. Attribute queries
3. Annotation queries

Rendering Z-Score in Methylation context
Any one of the combined Z score, the methylated Z score, and Unmethylated score, as well as Batman
algorithm results, can now be chosen for display. Earlier, only the first option was available.

Select Scale For Rendering
The scale ranges can now be selected from the “View Preferences” dialog.

Set Global and experiment context Array Name from SAF Row
This functionality enables one to:
1. Change the names of the arrays displayed inside an experiment
2. Change the names of the arrays displayed in the data node globally for a set of arrays
3. Have different names for a same set of arrays in different experiments; i.e different names for same
arrays that are included in multiple experiments
4. Be able to name the arrays, after the experiment is created, by a specific attribute chosen

View Tab Reorganized
In DNA5.0, many of the view options/menus are present in the Preferences dialog plus View tab. For
AGW 6.0 release, these have been reorganized, so that all the view options are managed from one place,
the “View Preferences” dialog.

Workflow Changes
User are able to create, save, edit, and delete workflow and analysis methods. Reports and Output
options are detached from analysis method and are now part of workflow.

Aberration Filter Changes
Aberration filter now has an option to split the nested aberrant intervals . This split happens when the
child interval gets filtered out on height criterion( e.g. a small amplified interval within a bigger deleted
interval) but the parent interval (bigger deletion) passes the criterion. In this case the parent interval is
split into two separate intervals and these two splits are reported as separate intervals. In such cases the
results of aberration filter would be different from previous version.

Intra Array Replicate Combine Changes
In previous version of DNAAnalytics, we were considering probes as a replicate probes if the start
positions were matching. In DNAAnalytics 6.0, 2 probes are considered as replicate probes if there start
and stop positions match.
Preloaded Data in DNAAnalytics 6.0
These are the datasets that are preloaded into the DNA Analytics 6.0 application:
Type
AMADID
Genome Build
CGH
014698
Hg18
# Probes
(Size)
99902
FE Files
1. US22502705_251469814934_S01_CGHv4_95_Feb07_1_1
2. US22502705_251469814934_S01_CGHv4_95_Feb07_1_2
3. US22502705_251469814935_S01_CGHv4_95_Feb07_1_1
4. US22502705_251469814935_S01_CGHv4_95_Feb07_1_2
The microarrays will be visible in the navigator when 014698 catalog design is completely downloaded
into the application.
System Requirements for Agilent Genomic Workbench 6.0
server
Windows XP or Windows Vista with Pentium 4 or later (server installation is supported on both 32- bit and
64- bit. Recommended configuration is 64 bit)
 Processor: Intel Core 2 Duo CPU
 Available Memory (RAM): min 8 GB
 Hard Disk Space:
100 GB - for MySQL
200 GB - for Common Storage
 Internet Connectivity: T1 or T3 connection (1.5 Mbps)
 If MySQL is already installed on the computer, make sure it is version
5.1 Pro.
Otherwise MySQL will be installed with Genomic Workbench. MySQL server configuration is
done automatically during the installation of Agilent Genomic Workbench Server software
System Requirements for Agilent Genomic Workbench 6.0
Client Software
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Windows XP or Vista with Pentium 4 or later
2GHz CPU or greater, dual core CPU recommended
4GB RAM minimum (need more when working with 244K or higher microarrays)
40GB Free Disk Space
1280x768 Display minimum
Tips on using Agilent Genomic Workbench Client Software
1. Array design import has three steps
Symptom: The manual has not fully explained the steps and icon changes for design importing.
Workaround: Step (1) GEML download: such as FE importing a design file. This is adequate for FE to
use, but not for AGW to use. In the Home design pane, the design has a yellow arrow;
Step (2) eArray is downloading the design. This is still not ready for AGW (see issue 16). In the Home
design pane, the design has a green arrow;
Step (3) Design is fully downloaded with genome build. This is now ready for all AGW needs. In the
Home design pane, the design has a green arrow and a sub-node “Design Samples” with the genome
build. If node does not appear after a long interval, try to close the application and re-launch.
2. Vista: need to change install directory
Symptom: The software will not install correctly on Vista machines without the correct install directory.
Workaround: User needs to make an install directory, with full permissions.
3. Vista: user.home property not set correctly
Symptom: Sometimes, the user home directory value is wrongly set on Vista. Due to this, many
processes like workflow will not function as they require user settings file which is located at user home
directory. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6519127.
Workaround: User needs to get the user home directory corrected by authorized system administrator.
4. Change memory settings, if necessary
Symptom: Sometimes, the user can change the memory settings to speed up the processing.
Workaround: If you want to maximize the speed of processing, you can change the memory setting for
the “heap size” of several processes. The heap size is controlled by two flags, –Xms<size> and –
Xmx<size>. JVM starts with -Xms amount of memory and can grow to a maximum of -Xmx amount of
memory. The 32-bit machine JVM does not support over 1400MB.
To change memory settings for running DNA Analytics 6.0
1.
In Notepad, open the file “.../Program Files/Agilent/Agilent Genomic Workbench Standard
Edition 6.0/ Agilent Genomic Workbench Standard Edition 6.0.lax”.
2.
Find the line “lax.nl.java.option.additional=-Xms1024m -Xmx1400m Dsun.java2d.noddraw=true”.
3.
Change the flags to your preferable memory setting. For example, if you have 2 GB RAM,
change the line to read “lax.nl.java.option.additional=-Xms1400m -Xmx1400m Dsun.java2d.noddraw=true”.
Note: Make sure the letter m is present at end of size and there is no space between
the number and m.
To change memory settings for Workflow mode
1.
In Notepad, open the file “.../Program Files/Agilent/ Agilent Genomic Workbench Standard
Edition 6.0/config/config_workflow.properties”.
2.
Find the property, HEAP_SIZE=-Xmx1200m.
3.
Change “1200” to your preferable memory setting. For example, if you have 2 GB RAM,
change the property to HEAP_SIZE=-Xmx1400m.
To change memory settings for the background process for importing FE data files
1.
In Notepad, open the file “.../Program Files/Agilent/ Agilent Genomic Workbench Standard
Edition 6.0/config/config_FEImport.properties”.
2.
Find the property, HEAP_SIZE=-Xmx512m.
3.
Change “512” to your preferable memory setting as you did for Workflow mode.
5. User may encounter an error message “Could not create Java Virtual
Machine Error”
Symptom: There is a known incompatibility between Agilent Genomic Workbench (AGW) versions 5.0
and 6.0 and Microsoft's Application Compatibility Toolkit (ACT) Version 5.5 (MS ACT). Installing MS ACT
will result in an error, "Could not create the Java virtual machine", which is displayed when attempting to
launch AGW.
Workaround: Uninstalling MS ACT 5.5 will return functionality to AGW.
.
Bug Fixes and Known Issues
Known Issues in eArrayXD
1. HD data sync doesn’t happen when HD data updated on production
2.
Symptom
HD data sync does not happen when HD data is updated on the eArray website.
Fix/Workaround
User can give HD searches again to get new HD data.
Notes
Team track id - 07108
'Import Custom Genome for Tiling' is not available in CH3 application space
Symptom
User will not be able to Import custom genome for tiling in CH3 application
space.
Workaround
Users can import their custom genome in ChIP/ CGH/ SureSelect
TargetEnrichment application. This custom genome will be available for tiling in
CH3 application space.
Notes
Team track id - 07101
3. Array Layout Visualization: Slide view is not proper for 8 X 15 and 8 x 60 format
4.
Symptom
If user selects a 8x15 or 8x60 array design for array layout visualization, the
slide borders are not clearly visible in the visualization.
Fix/Workaround
None
Notes
Team track id - 07093
Performance issues in some functionalities
Symptom
Fix/Workaround
Performance is slow in below mentioned functionalities
 Probe Download
 Probe Group download

Exon Interval Finder
None
Notes
Team track ids –
06678,07089, 07084
5. Simple probe search – not working on ‘All’ option
Symptom
Simple probe search – If user tries to search on “ALL” search type, user is
prompted with message ‘Please give search term’
Fix/Workaround
User can give exact term in edit box and search to get the results. Or he can
select specific search type from the search type drop down.
Notes
Team track id - 7109
Bug fixes in Feature Extraction 10.9

Find feature not working for non Agilent arrays (TT 2149).

FE installation with MySQL fails for MySQL version 5.1 (TT 2188).

Abs functionality not working (TT 2320).

Some arrays do not have any found spots -- broken statistics.(TT 2227).

"Copying JRE files" window should be hidden during installation (TT 2187).

Assigning default protocols automatically (2175).
Known Issues in Feature Extraction 10.9

MySQL ODBC connector 5.1 is not supported (TT 2322).

Sometimes the automation icon does not appear for extraction set (TT 2356).

OK button on grid template disabled only during Dyenormlist launch.This would
allow users connected from other clients to delete grid template after dyenomlist is
launched (TT 2360).

Left out of the command line chapter, chapter 6 of the FE Reference guide
is a warning that has been added to the software. All of the error and warnings
the software can produce while extracting an array are listed at the end of that chapter.
The warning we missed says “Agilent does not support this configuration,
please consult the support matrix in the Feature Extraction users guide for a
supported configuration”.The warning ID for this is 1060. Note that when refer
users to the users guide,the configuration information is explained on page 19.

Grid mode save grid does not allow projects to be run. User has to
close grid mode after the grid has been saved before FE will correctly update
the project explorer and allow the project to be run (TT 2310).

Changing the color scale does not work while in grid mode.If User
attempts to change color scale from “All Channels” to “Red Channel” or
“Green Channel” it does change (TT 2309).

The 1-color QC report has page break problems causing one of the pages
to break across a table when the QC report in put into PDF mode (TT 2299).

The older version of easy PDF, easy PDF 5 not uninstalled on upgrade
to FE 10.7. This is because we have moved to easy PDF 6 and the upgrade installer
doesn’t correctly handle uninstalling the old component. Work around is to delete
the easy PDF 5 printer directly through Start->Settings->Printers and Faxes.
The instance of easy PDF 5 does not create any problems for FE 10.7 extractions
(TT 2292).

Attempting to extract an Axon Scan without a barcode, grid template/
grid file or protocol will crash Feature Extraction requiring the machine to
reboot (TT 2289)

Extraction automation does not work for Agilent cropped multiplex images.
This is because we adorn the pack information on the barcode so it doesn’t get
lost when the image is cropped (TT 2287).

Trying to extract a third party array by putting an Agilent barcode inside
the tiff image will lead to the software failing with a low level runtime error
(TT 2272).

The eArrayXD integration feature is not quite complete in that after FE runs,
the project explorer is not updated to reflect which grid template and protocol was
automatically assigned.This can be confusing to user after the project has finished
as they do not get the feedback in the Project Explorer (TT 2236).

Sometimes for arrays from designs that have high numbers of ignore features
the user will get “INFO:(Array_1_1) This array doesn't have any found spots.
Maybe the array has not been hybridized.” The calculation that generates this message
is not correct (TT 2227).

Flip functionality fails with a poor error message if not enough disk space
is available to complete the operation.The error message reads "Save as failed due to
unknown reasons".(TT 2210)

For CGH, and GE2 QC reports, the log ratio spatial plot has errors in sampling.
Currently, if there are > 3500 significant Up or Down-regulated log ratios, then the
code does a sampling. This leads to a confusing appearance of the number of up and
down regulated features (TT 2207).

After a scan is generated, the image should retain the parameters by which it
was generated, and they should be retrievable from the Feature Extraction menu item
Image File Info...,which displays the Scan Image Properties window. Parameters that
are currently missing include:
Single pass or Double pass
16-biit or 20-bit
Laser set points and/or actual laser power readings for each channel
(this should reflect compensation, if invoked)
PMT compensation factor
PMT Calibration Error flag status (TT 2203)

For new format scans, on 64 bit OS PCs, the first submenu option i.e "Flip
upper left to lower Right"(Landscape/portrait) and save" is not completely shown (TT 2190).

QC report contents can appear broken in that tables and graphs don’t fit on
to the pages all that well.The workaround is to adjust the printing margins in internet
explorer if the user is using I.E. 6.0. We have not seen the issue under IE 7 or later (TT 2179).

For miRNA applications sometime you can get some weird looking %CV of the
replicated probes plot on the miRNA QC Report if there are no CVs to plot. This
can happen if we can not calculate any replicate %CVs because the data is not good enough (TT
2171).

For new format scans while setting color ranges, the ability to adjust colors
in high fidelity mode can lead to errors – namely if the user tries to set
“Auto Scale Image” after unsetting this option. (TT 2166).

If a user attempts to import a grid template during an extraction run,
the grid template may fail to properly import into the software. The work around is to only
import grid templates when a project is not running. (TT 2112).

Attempt to abort an extraction on Vista 64 will cause the extraction to stop
ungracefully with a low level runtime error (TT 2092).

The eArray automatic online protocol update can fail if the either the protocol
or the metric associated with that protocol are missing (but not both) when the update occurs.
It is possible to make this happen because even read only protocols and metric sets can be
removed using FeNoWindows. The worst case is if the metric set is missing from FE, then the
eArray will fail to update the protocol due to a missing metric set (TT 2075).

Sometimes in rare instances, the switch to configure mode button will not be
enabled after the extraction is complete. The extraction will have to be closed and
re-opened to enable to config / run mode toggle (TT 2069).

The grid template that is currently in use during an extraction,can be removed causing
the extraction to fail (TT 2042).

The eArray configuration setting “Automate FE extraction by automatically downloading
design files from eArray” can cause unwanted behavior, if user wishes to extract an image
using a grid template with an AMADID doesn’t match the image’s AMADID. Disabling the eArray
configuration setting temporarily causes FE to behave correctly in this case TT 2040).

Attempting to calculate spot size and centroids in manual grid mode using a high
resolution scan of a third party array will cause FE to crash (TT 2032).

In rare instances the QC report can fail to generate. This is true when 30u feature
size 2-pack arrays are used in FE, using a CGH protocol that generates an old style CGH
QC report. For the 2-pack 30-micron feature size arrays the new streamlined CGH QC report
must be used (TT 2019).

It is not recommended to run projects containing multiple extractions directly
through FeNoWindows.Projects containing multiple 30-micron feature size 1 million feature
array will run out of memory if run directly using FeNoWindows. The work around is to
either use the FE GUI to run these projects or to break up the project into multiple
projects each containing 1 extraction (TT 2016).

Do not remove the DBConnectInfo.ini file from the FE installation folder. If
that file is not available the software cannot be removed via the install or Add/Remove
programs (TT 1944).

When viewing shape files, feature outliers are not visible until the image is
zoomed or cropped (which effectively zooms) (TT 1955).

Viewing the scan properties can cause the image to appear distorted.Minimizing
followed by reopening the image will correct the issue (TT 1959).

Scans of 2, 3 and even 5 micron resolution using full sized scan regions are
quite large creating memory issues for the software.In order to address memory and
performance issues the following restrictions are true about the imaging.
The new view window feature (with Ctrl-N as the shortcut) that allows users
to open one channel of the scan will not work for new format scans.
When cropping a new format scan to view the image close up, what FE refers to
as high fidelity mode,zoom out is disabled below 200%.
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When creating a grid file of Agilent arrays some annotation columns may be lost.
Currently only the primary annotation columns are certain to make it into the grid file.
Those annotation columns are Probe Name, Systematic Name, and Gene Name. Other annotation
fields are not certain to be output. There is no workaround to this issue (TT 1917).
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For large grid templates using the dye normalization list editor can take a very
long time.This is a function of the number of probes that have to read from the database
and loaded into the editor.It is possible to create the lists outside of FE and load them
into the software without using the list editor.Please consult the FE manual for details
(TT 1913).
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Blank fields, namely blank annotation fields above and beyond the primary
annotation fields of Probe Name, Systematic Name, Gene Name, used inside of the GEML xml
design files will fail to load into the MySQL database.(TT 1912 and 1853).
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Under Windows Vista, FE users may not have permission to write to certain
directories or overwrite certain files.This will cause FE to fail to load grid templates,
protocols and/or metric sets. Also it will cause FE to fail to process extractions.
The solution to this is to make sure the User Access Controls are turned off and ensure
that C:\Program Files\Agilent\MicroArray\FE\Temp is writable and empty (TT 1836).
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It is possible using the FE to remove a grid template while the software is
processing extractions.This is not recommended as it could cause the project to fail
if that grid template is used (TT 1826).
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Applying many different image manipulations including Flip and Rotate on 5
micron 16-bit scans may cause FE to run out of memory and yield the message "Failed
to load bitmap". The workaround is to close the FE software re-open it and try the
operation again (TT 1874, 1768, and 1766).
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Protocols that are loaded into the database by name are specifically not
case sensitive but protocols specified in the project are case sensitive.
Please keep all protocol names the same case (e.g. stick with capital letters) (TT 1699).
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When cropping an image using the new crop image dialog, the file name is
appended with 1_1 although "Cropped multiplex" is not selected (TT 1679).

When running an XDR extraction project, the summary report can give grid placement
error ‘… The spot centers are shifted relative to their nominal grid.' But the QC report
says the grid is normal. This is an indication that XDR failed to properly extract the
low PMT scan and there may be an issue with the image registration (TT 1675).

When a two-channel tiff file is split into two single-channel tiff files (one
for Red and one for Green) from the Agilent Microarray Scanner, On-Time project treats the
split tiff files as two separate single-channel files (TT 282).

Protocol, DyeNormList, or GridTemplate cannot have special characters in the name
or description. The character that is sure to break is"'"(TT 652 & 657).

FE is not designed to support concurrent users. The software will only allow one
user to user FE at a time.If another user is logged into the same machine, only one will
be allowed to run FE.
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You cannot open a .tiff image from a CDROM or DVD. Copy the image to a hard disk
or network share.
Known Issues in QC Tool
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Quality objects: can be deleted by non-owners (TT 1929).
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QC table: not sorting by ExtractionTime correctly (TT 2175).

ExtractionStatus,QCReportType and ColorMode will be shown in integer format when exported to a
file (TT 2497).
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The queries, metric sets, and charts are not ordered in alphabetical order in the navigator panes (TT
2520).
Known Issues in Workflow Manager

When "Output location same as image" option is chosen then output files are generated in the same
level as image, rather than in a workflow-generated folder on the same level as the image (TT 2393).

When doing an extraction in the workflow mode, you may get a security alert concerning Java binary
files. When prompted, choose "Unblock" to allow the workflow to continue. You may resolve this by
changing your firewall security options (TT 1962).
Bug fixes in DNAAnalytics 6.0
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Cursor is shown at different position in the table & UI.
Log Ratio - "Select Scale of Rendering".
Color code of Signal Intensities does not make sense.
Common aberration/Filter issue – needs change in interval tree structure and alg.
Table coloring not getting refreshed after applying/removing aberration filter.
CH3 & ChIP Ribbons: accelerator keys.
Workflow: FE Pref's needs to be version neutral & not needed as icon.
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Switch Application boxes.
Scatter plot not re-drawing correctly after signal filter added.
Switch Application functionality.
Workflow Report: "Overwrite = False" bug.
AnalysisMethod: SaveAs should start with current name.
Sample Manager Array Data navigation pane: improper use of Demo node.
Save Workflow dialog should be Save Analysis Method.
ChIP QC_Report & QC_Metric need re-naming.
Attribute file: non-editable fields inconsistent.
Attributes File Importer: Incorrect Header logic
Running cyto report by run by importing option gives error.
Application gives error if you keep the application ideal for 3-4 hours.
Error will occur, if you apply expand after applying moving avg on expt.
EXP design is missing in the default CGH-EXP expt. ADM2/HMM getting applied.
Expand is not working for catalog data.
Create gene list option is not showing the selected row chromosome.
Workflow: need to be able to Save and have persistent file.
Import Attribute File with incorrect predefined fields yields incorrect import.
Attribute file export incorrect when multiple Genome Builds are present.
Track order does not change in the navigator.
UserPref dialog: click Cancel should clear previous changes.
Attribute File with replicate names does not import correctly.
Aberration get disappeared from the UI after applying Moving avg on experiment.
When you aberration filter the table few is not always updated.
Axon files should have design type as CGH/ChiP depending on context and not axon.
In the open application tab, eArrayXD application button is always disabled.
Aberration filter should be modified to fix a couple of existing issues.
Import Filter menu is missing.
Empty Probe report is getting generated for single design experiment.
Sample Manager table does not stay in sync.
chrM is labeled wrongly in chromosome view.
HMM results are not generated for all the arrays in the experiment.
Sample information not passed to QC report from a workflow.
Experiments created from workflow that failed.
Wrong chromosome displayed in chromosome view.
ADM-2 does not work on combined dye flip array.
When applying the default feature filters, the moving average of the first subarray is disappearing on
chromosome Y.
Known Issues in DNAAnalytics 6.0
1. Combine Track logic
Symptom
In this release operations for combining tracks work by assuming the
track to be sets of intervals but do not perform any operations on
intervals themselves . For example if a track consists of intervals e1, e2
and another of interval e2 , e3 then the logic of intersection would result
in a track with just e2 . However if a track has interval e1 and another
track has interval e2 where e2 is contained in e1 then the intersection
would not give common part e2 but rather result would be empty and a
message no annotations found would be shown
Fix/Workaround
Notes
None
None
2. Cyto Report keeps running for Use Workspace Settings on HMM
Symptom
Steps:
1. Create an Experiment and apply Aberration witth HMM Alogorithm.
2. Create a Cyto Template with option "Use Workspace Settings" selected in
Analysis Settings tab.
3, Run the same cyto report. The report keeps running
Fix/Workaround
Notes
None
None
3. If any gene list is applied, Aberration in all the views gets updated except in the table
Symptom
Fix/Workaround
Notes
Apply gene list functionality is not working on the data table. The gene list only
gets applied on the aberrations in the views.
None
Apply gene list only influences the display and not the actual aberration result.
4. Attribute values set by one user are not getting updated for the other users in the same session
Symptom
Fix/Workaround
Notes
Array attribute values updated by one user are not visible to other users in the
same session. Other users have to restart the application to see the updated
values.
Restarting the application will show the updated attribute values.
None
5. Navigation nodes are not opening/collapsing correctly
Symptom
Fix/Workaround
Notes
At times, data nodes in the navigator do not expand or collapse.
Changing the application context and switching back will resolve the issue.
None
6. Application becomes very slow after you apply lowess OR variance stabilization with intra array.
Symptom
Fix/Workaround
Notes
Chip Context > Application becomes very slow after you apply lowess OR
variance stabilization with intra array. If you remove intra array, the application
again work properly.
Another observation: In case all the normalizations are applied in one step, then
it takes a very long time. Instead if you apply all the normalizations one by one,
it takes much less time.
None
None
7. Issues with high density ChIP designs:
Symptom
If a million feature ChIP-on-chip design has most of the probes on a few
chromosomes only, then analysis may have certain issues.
1. With those designs ChIP workflow also may fail. The probe report may
not be generated and application may yield “Out of Memory” error.
2. Fusing two or more such designs will cause analysis to fail.
Fix/Workaround
Notes
None
None
8. Colored filled circle looks like a square.
Symptom
Fix/Workaround
Notes
Colored filled circle symbols in gene view looks like squares in the scatter plot
views
None
None
9. Number of probes in the report (except interval based text aberration report) includes failed probes.
Symptom
Fix/Workaround
Notes
If feature filter is applied, then filtered probes are considered in the reported
aberrantion intervals.
None
None
10. Users are recommended to download the design files first before running workflow.
Symptom
Fix/Workaround
Notes
If the design is not already downloaded and available to DNAAnalytics,
1. Sometimes workflow fails as FE cannot get the grid template for
extraction.
2. For Analysis workflow sometimes is stuck in the design verification step
Design needs to be fully downloaded with genome build node before starting a
workflow
The genome build is a sub-node under the design node
11. OutOfMemoryError while restoring auto created experiment from workflow with 100 1 million feature
data
Symptom
Fix/Workaround
Notes
OutOfMemoryError while restoring auto created experiment from workflow with
100 million feature data
None
None
12. Workflow for fusing catalog data fails if design level filter is applied.
Symptom
Fix/Workaround
Notes
Create workflow to fuse catalog design data.
Now in the run analysis settings apply design filter.
Run the workflow.
Actual result: Workflow will take too much time and it will fail.
None
None
13. Some operations may take a long time when you use a catalog design for the first time.
Symptom
When catalog design data is used for the 1st time in an experiment then some
Fix/Workaround
Notes
operations, which needs different column data for that design, may take long
time for certain operations. But next time onwards, if you use any data set of that
catalog design, the operations will be very fast.
None
None