Feature Extraction Software

ÐÏ à¡± á > þÿ 4 6 þÿÿÿ 3 € ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿì¥Á % ð ¿ Û bjbj%ç%ç -. ÿÿ G• G• Û ÿÿ ÿÿ l ¸ ¸ ¸ ¸ Ä $ • ¶ ô ô ô s ä ô - B ô - ô ô ô ô ô - - B ô ô ô ô ô ô W ô ô ô è $ S ô °º‡í]ØÄ œ ¸ m 0 • W W ´ < ð , Ù to Agilent Image Analysis & Feature Extraction Software Self-Assessment Test Introduction 1. Explain how to access the version number of the Image Analysis & Feature Extraction Software. 2. Demonstrate how to crop and save a microarray scan image. 3. Explain the default method for scaling the color range 4. Explain how to set the design file search path 5. Describe the required Feature Extraction input files 6. Describe the Feature Extraction output files 7. Explain the Agilent Slide Barcode nomenclature 8. Explain the Agilent Microarray Identifier nomenclature 9. Explain the Agilent Design and Printing File naming nomenclature 10. Demonstrate how to manually store the microarray identifier within the scan image file. 11. Demonstrate how to manually specify a design file. 12. Demonstrate how to manually locate the microarray corners, if automatic corner finding fails. Introduction to Agilent Image Analysis & Feature Extraction Software Answers to the Self-Assessment Test 1. Explain how to access the version number of the Image Analysis & Feature Extraction Software. Click Help > About Analysis. 2. Demonstrate how to crop and save a microarray scan image. To crop an image: Left-click and hold the mouse button. Draw a box around the microarray – leave a border of 2-3 feature-widths. Release the mouse button. The cropped image appears in a new window. To save the cropped image: Click the “Save Cropped View” icon or click File > Save Cropped View. Complete the information in the Save Cropped View dialog. 3. Explain the default method for scaling the color range The red and green color channels are scaled independently from each other. For each color channel: The pixel intensity values corresponding to the first and 99th percentiles are determined. All pixels having intensities lower than the first percentile are displayed at the first percentile value. All pixels having intensities higher than the 99th percentile are displayed at the 99th percentile value. This method compresses the data range and makes the scan image appear brighter. The underlying pixel intensities (the raw data) are not changed, and therefore the resulting gene expression profile is unaffected. 4. Explain how to set the design file search path Click Options > set design file search path Specify the directory location of the design file 5. Describe the required Feature Extraction input files a. Design (Pattern) file – provides the feature extraction software with the location and gene identity of every feature on the microarray. b. Printing file (for cDNA microarrays only) – provides a list of features whose clones were flagged as bad during the QC process. Data from these features are ignored when generating the gene expression profile. c. Scan image – the red and green pixel intensities are used to measure differential expression for each feature. This data is combined with the information in the design file (and printing file for cDNA arrays) to generate a gene expression profile for the microarray. 6. Describe the Feature Extraction output files a. XML – contains the gene expression profile in GEML format. Expression data in this file format can be loaded directly into the Rosetta Resolver Gene Expression Analysis software. b. Tab-Text – contains the gene expression profile in tab-text format and is intended for customers who are not using Resolver. The data will load into third-party gene expression analysis software with a minimum of manipulation. c. Visual Results – contains the “shapes” annotation generated by the Feature Extraction software. This enables subsequent viewing of the “shapes” annotation without having to re-extract the scan image. 7. Explain the Agilent Slide Barcode nomenclature The Agilent barcode standard consists of 14 digits: Digit 1 – version of the barcode format Digit 2 – number of digits in the design identifier field (currently 6) Digits 3 to 8 – design identifier Digits 9 to 14 – serial number 8. Explain the Agilent Microarray Identifier nomenclature The microarray identifier is based on the slide barcode, A suffix is appended to the slide barcode to uniquely identify each array on the slide. Suffix _A01 indicates a 22K-feature microarray for slides with one microarray, or the left array for slides with two microarrays. Suffix _A02 indicates the right array for slides with two microarrays. 9. Explain the Agilent Design and Printing File naming nomenclature Design and printing file names are based on the design identifier and date. Printing files are only generated for cDNA microarrays. Customers should not rename these files. Nomenclature is design_D_date.xml for design file and design_P_date.xml for printing file. Example: 012345_D_20020324.xml indicates a design file for design id 012345, generated on March 24, 2002. 10. Demonstrate how to manually store the microarray identifier within the scan image file. If the slide barcode was not properly read by the scanner, the user must manually input the slide barcode when saving a cropped scan image. After the user inputs the design identifier and serial number in the Create Barcode dialog, she can save the cropped scan image. 11. Demonstrate how to manually specify a design file. If the design file is not in the design file search path, the Load Design File dialog will prompt the user to browse to the design file. Slide printing files can not be loaded using this method and therefore, no information on bad clones will be available. Note that if the manuallyspecified design file does not represent the microarray in the scan image, an erroneous gene expression profile will result. 12. Demonstrate how to manually locate the microarray corners, if automatic corner finding fails. Zoom in on the top-left corner feature on the microarray. Place the mouse over the center of the corner feature and left-click. Click the enter button for Upper Left in the Find Spots tab of the Feature Extraction user interface. Repeat for the upper-right and lower-left corner features. 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r k s p a c e s / T r a i n i n g / P u b l i c / 0 3 0 9 6 0 u h t t p s : / / e x t r a n e t . c h e m . a g i l e n t . c o m / L i b r a r y / T r a i n i n g / P u b l i c , h t t p s : / / e x t r a n e t . c h e m . a g i l e n t . c o m / L i b r a r y / T r a i n i n g / P u b l i c E n g l i s h U I n F G E S o ß G E S o I t t e k n F e ; N I T E D f o r m a t T r a i n - 1 - 0 0 2 f w a r e T r a i n - 1 - 0 0 2 f w a r e a l s o s t i n o w l e d g a t u r e # F e a t u H A R T N ; # L i f 7 7 5 8 A m e r i c a s <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration S i i - T c n A A T E S ; # S o f t w a r e & s ; # ; # B i o s c i e n c e ; # g m a t e r i a l o f t h e A N - C E : F e a t u r e E x t r a c t i o n ; # G e n o m i c s ; # i n g m a t e r i a l o f t h e A N - C E - A : F e a t u r e E x t r a c t i o n B a s i c O p e r a t i o n T r a i n i n g . i n c l u d e s t h e S e l f - A s s e s s m e n t o r d e r t o c h e c k y o u r e a b o u t I m a g e A n a l y s i s E x t r a c t i o n S o f t w a r e . r e E x t r a c t i o n S o f t w a r e ; # E T T , M A R K ( A - U S A , e x 1 ) e S c i e n c e s I n f o r m a t i c s ; # & B A L D W I N , V I C T O R I A ( N o n - A , e /> value="NMR Consoles"/> value="NMR Magnets"/> value="NMR Probes"/> value="NMR Spectrometers"/> value="Nucleosil Columns"/> value="Offgel"/> value="Oligo aCGH"/> value="Peptide Cleanup Pipette Tips"/> value="Peptide Cleanup Spin Tubes"/> value="Physical Testers"/> value="Pipette Tips"/> value="Portable Leak Detectors"/> value="Prep LC"/> value="Preparative Columns"/> value="Prep-Process Benchtop LC Detectors"/> value="Prep-Process Benchtop LC Fraction Collectors"/> value="Prep-Process Benchtop LC Injectors"/> value="Prep-Process Benchtop LC Systems"/> value="Prep-Process Benchtop LC Valve Solution"/> value="Prep-Process LC Pumps"/> value="PrepStat"/> value="Process LC Systems"/> value="Processing Hardware"/> value="Protein"/> value="Protein Sequencing"/> value="Protein System"/> value="Proteomic Consumables"/> value="Proteomics Accessories"/> value="Purospher Columns"/> value="Robotic Automation"/> value="Rotary Vane Pumps"/> value="RPS Series Roots Pumping Systems"/> value="RRHT"/> value="Sample Device"/> value="Sample Filtration"/> value="Sample Introduction"/> value="Sample Preparation"/> <xsd:enumeration value="Sampling Systems"/> <xsd:enumeration value="SampliQ QuEChERS"/> <xsd:enumeration value="SampliQ SPE"/> <xsd:enumeration value="Search"/> <xsd:enumeration value="Selective Detector"/> <xsd:enumeration value="Small Molecule System"/> <xsd:enumeration value="Software"/> <xsd:enumeration value="Software Compliance"/> <xsd:enumeration value="SPE (Solid Phase Extraction)"/> <xsd:enumeration value="SPE Cartridge Reservoirs and Stopcocks"/> <xsd:enumeration value="SPE Method Development Kits"/> <xsd:enumeration value="Specialized"/> <xsd:enumeration value="Spectrometry Data System"/> <xsd:enumeration value="Spectroscopy Data System"/> <xsd:enumeration value="Spin Concentrators"/> <xsd:enumeration value="Spin Filters"/> <xsd:enumeration value="Spin Tubes"/> <xsd:enumeration value="Superspher Columns"/> <xsd:enumeration value="SureSelect"/> <xsd:enumeration value="Synthesizer"/> <xsd:enumeration value="Syringe Filters"/> <xsd:enumeration value="Syringes"/> <xsd:enumeration value="Systems"/> <xsd:enumeration value="Thermostat Column 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nillable="true" ma:displayName="Product" ma:hidden="true" ma:internalName="Product"> <xsd:complexType> <xsd:complexContent> <xsd:extension base="dms:MultiChoice"> <xsd:sequence> <xsd:element name="Value" maxOccurs="unbounded" minOccurs="0" nillable="true"> <xsd:simpleType> <xsd:restriction base="dms:Choice"> <xsd:enumeration value="G2912A"/> <xsd:enumeration value="G2613A"/> <xsd:enumeration value="G2614A"/> <xsd:enumeration value="G2630A"/> <xsd:enumeration value="G2630B"/> <xsd:enumeration value="G2855B"/> <xsd:enumeration value="G2888A"/> <xsd:enumeration value="G2913A"/> <xsd:enumeration value="G2916A"/> </xsd:restriction> </xsd:simpleType> </xsd:element> </xsd:sequence> </xsd:extension> </xsd:complexContent> </xsd:complexType> </xsd:element> <xsd:element name="IndustryGroup" ma:index="27" nillable="true" ma:displayName="Industry Group" ma:description="Select only the Industry Group that is the primary focus of this content." ma:hidden="true" ma:internalName="IndustryGroup"> <xsd:complexType> <xsd:complexContent> <xsd:extension base="dms:MultiChoice"> <xsd:sequence> <xsd:element name="Value" maxOccurs="unbounded" minOccurs="0" nillable="true"> <xsd:simpleType> <xsd:restriction base="dms:Choice"> <xsd:enumeration value="BioPharma"/> <xsd:enumeration value="Clinical Research"/> <xsd:enumeration value="Energy & Fuels"/> <xsd:enumeration value="Environmental"/> <xsd:enumeration value="Food Testing & Agriculture"/> <xsd:enumeration value="Forensics & Drug Testing"/> <xsd:enumeration value="Genomics"/> <xsd:enumeration value="Geochemistry, Mining & Metals"/> <xsd:enumeration value="Homeland Security"/> <xsd:enumeration value="Integrated Biology"/> <xsd:enumeration value="Materials Testing & Research"/> <xsd:enumeration value="Metabolomics"/> <xsd:enumeration value="Pharmaceuticals"/> <xsd:enumeration value="Proteomics & Protein Sciences"/> <xsd:enumeration value="Semiconductor Analysis"/> <xsd:enumeration value="Specialty Chemicals"/> <xsd:enumeration 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<xsd:enumeration value="Fuel Cells"/> <xsd:enumeration value="Genomics"/> <xsd:enumeration value="Homeland Security"/> <xsd:enumeration value="Hydrocarbon Processing"/> <xsd:enumeration value="Nucleic Acid Analysis"/> <xsd:enumeration value="Production-QA/QC"/> <xsd:enumeration value="Proteomics"/> <xsd:enumeration value="Semiconductor"/> <xsd:enumeration value="Specialty Chemical"/> </xsd:restriction> </xsd:simpleType> </xsd:element> </xsd:sequence> </xsd:extension> </xsd:complexContent> </xsd:complexType> </xsd:element> <xsd:element name="Industry" ma:index="29" nillable="true" ma:displayName="Industry" ma:hidden="true" ma:internalName="Industry"> <xsd:complexType> <xsd:complexContent> <xsd:extension base="dms:MultiChoice"> <xsd:sequence> <xsd:element name="Value" maxOccurs="unbounded" minOccurs="0" nillable="true"> <xsd:simpleType> <xsd:restriction base="dms:Choice"> <xsd:enumeration value="Air"/> <xsd:enumeration value="Analysis of Process Chemicals"/> <xsd:enumeration 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value="FAQs"/> <xsd:enumeration value="Installation and Maintenance Videos"/> <xsd:enumeration value="Illustrated Parts Breakdowns"/> <xsd:enumeration value="Informatics and Software"/> <xsd:enumeration value="Instruments & Systems"/> <xsd:enumeration value="Life Sciences"/> <xsd:enumeration value="Reagents, Standards & Kits"/> <xsd:enumeration value="Software Familiarization Videos"/> <xsd:enumeration value="Parts Information"/> <xsd:enumeration value="Pharmaceuticals"/> <xsd:enumeration value="Services"/> <xsd:enumeration value="Support Services"/> <xsd:enumeration value="..."/> </xsd:restriction> </xsd:simpleType> </xsd:element> </xsd:schema> <xsd:schema targetNamespace="d60c28fc-3d14-46f3-b174-9a10a2a6c6f4" elementFormDefault="qualified" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:dms="http://schemas.microsoft.com/office/2006/documentManagement/ty pes"> <xsd:import namespace="http://schemas.microsoft.com/office/2006/documentManagement/ty pes"/> <xsd:element name="Analytical_x0020_Technique" ma:index="37" nillable="true" ma:displayName="Analytical_x0020_Technique" ma:format="Dropdown" ma:internalName="Analytical_x0020_Technique" ma:readOnly="false"> <xsd:simpleType> <xsd:restriction base="dms:Choice"> <xsd:enumeration value="Atomic Absorption (AA)"/> <xsd:enumeration value="Capillary Electrophoresis (CE)"/> <xsd:enumeration value="CE/MS"/> <xsd:enumeration value="Dissolution"/> <xsd:enumeration value="Fluorescence Spectroscopy"/> <xsd:enumeration value="FTIR"/> <xsd:enumeration value="GC"/> <xsd:enumeration value="GC Analyzer"/> <xsd:enumeration value="GC QQQ"/> <xsd:enumeration value="GC Q-TOF"/> <xsd:enumeration value="GC x GC"/> <xsd:enumeration value="GC/MSD"/> <xsd:enumeration value="GC-RapidMS"/> <xsd:enumeration value="GPC/SEC"/> <xsd:enumeration value="ICP-MS"/> <xsd:enumeration value="ICP-OES"/> <xsd:enumeration value="LC"/> <xsd:enumeration value="LC QQQ"/> <xsd:enumeration value="LC Q-TOF"/> <xsd:enumeration value="LC TOF"/> <xsd:enumeration value="LC/MS"/> <xsd:enumeration value="Micro GC"/> <xsd:enumeration value="MP-AES"/> <xsd:enumeration value="MS"/> <xsd:enumeration value="NMR"/> <xsd:enumeration value="PCR / qPCR"/> <xsd:enumeration value="Rapid-MS"/> <xsd:enumeration value="Thin Layer Chromatography"/> <xsd:enumeration value="UHPLC"/> <xsd:enumeration value="UV-Vis-NIR Spectroscopy"/> <xsd:enumeration value="X-ray Crystallography"/> </xsd:restriction> </xsd:simpleType> </xsd:element> <xsd:element name="Matrix" ma:index="38" nillable="true" ma:displayName="Matrix" ma:format="Dropdown" ma:internalName="Matrix" ma:readOnly="false"> <xsd:simpleType> <xsd:restriction base="dms:Choice"> <xsd:enumeration value="Biodiesel/Biogas"x 1 ) T r a i n i n g M a t e r i a l L i b r a r y /> <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration <xsd:enumeration value="Biofuel(s)"/> value="Biological Mass"/> value="Biologics"/> value="Blood"/> value="Bone"/> value="Breast Milk"/> value="Cell culture"/> value="Cereals"/> value="Coffee"/> value="Composites"/> value="Cosmetics"/> value="Dairy"/> value="Designer Drugs"/> value="Drinking Water"/> value="Drugs of 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value="Waste Water"/> <xsd:enumeration value="Water"/> <xsd:enumeration value="Wood"/> <xsd:enumeration value="Yeast"/> </xsd:restriction> </xsd:simpleType> </xsd:element> </xsd:schema> <xsd:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/ core-properties" elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all" xmlns="http://schemas.openxmlformats.org/package/2006/metadata/coreproperties" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:odoc="http://schemas.microsoft.com/office/internal/2005/internalDoc umentation"> <xsd:import namespace="http://purl.org/dc/elements/1.1/" schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd" /> <xsd:import namespace="http://purl.org/dc/terms/" schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms .xsd"/> <xsd:element name="coreProperties" type="CT_coreProperties"/> <xsd:complexType name="CT_coreProperties"> <xsd:all> <xsd:element ref="dc:creator" maxOccurs="1" ma:index="9" ma:displayName="Author"/> <xsd:element ref="dcterms:created" minOccurs="0" maxOccurs="1"/> <xsd:element ref="dc:identifier" minOccurs="0" maxOccurs="1"/> <xsd:element name="contentType" minOccurs="0" maxOccurs="1" type="xsd:string" ma:index="35" ma:displayName="Content Type"/> <xsd:element ref="dc:title" maxOccurs="1" ma:index="1" ma:displayName="Title"/> <xsd:element ref="dc:subject" minOccurs="0" maxOccurs="1"/> <xsd:element ref="dc:description" minOccurs="0" maxOccurs="1"/> <xsd:element name="keywords" maxOccurs="1" ma:index="7" ma:displayName="Keywords"> <xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:minLength value="1"/> </xsd:restriction> </xsd:simpleType> </xsd:element> <xsd:element ref="dc:language" minOccurs="0" maxOccurs="1"/> <xsd:element name="category" minOccurs="0" maxOccurs="1" type="xsd:string"/> <xsd:element name="version" minOccurs="0" maxOccurs="1" type="xsd:string"/> <xsd:element name="revision" minOccurs="0" maxOccurs="1" type="xsd:string"> <xsd:annotation> <xsd:documentation> This value indicates the number of saves or revisions. The application is responsible for updating this value after each revision. </xsd:documentation> </xsd:annotation> </xsd:element> <xsd:element name="lastModifiedBy" minOccurs="0" maxOccurs="1" type="xsd:string"/> <xsd:element ref="dcterms:modified" minOccurs="0" maxOccurs="1"/> <xsd:element name="lastPrinted" minOccurs="0" maxOccurs="1" type="xsd:dateTime"/> <xsd:element name="contentStatus" minOccurs="0" maxOccurs="1" type="xsd:string"/> </xsd:all> </xsd:complexType> </xsd:schema> </ct:contentTypeSchema>

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