tranSMART RC2 Release – Test Case (Working Document)
I.
Test identification
tranSMART instance
< tranSMART URL >
Test case
tranSMART_test_RNAseq
Description
Analyze and export RNA seq data with tranSMART
Successful End Condition
(Acceptance Criteria):
Open Issues:
II.
All the Test Steps of the ‘Test case’ should pass
none
Tester identification
Tester Name:
Tester’s Computer ID:
Tester User ID:
Tester Site:
tranSMART role(s) tester is assigned to:
Browser used for this test: FIREFOX
Testing start (date + time):
1 tranSMART_test_RNAseq
Testing end (date + time):
tranSMART RC2 Release – Test Case (Working Document)
III.
Test results
Objectives
Verify that analysis (‘Advanced Workflow’) can be generated with RNA seq data
Verify that RNA seq data sets can be exported out of tranSMART
Prerequisites
Role assigned to the tester’s user account: ‘Spectator’ (at a minimum)
Internet browser: Tester should have Firefox installed on his/her computer
Login: Tester should be able to launch the tranSMART application successfully (link provided on page 1 of this Test Case)
Test data: The study ‘RC2 testing\test_RNAseq’ should be available in the application with the following nodes:
\Data\RNAseq\RNA SEQ\Breast \Breast
\Design Factors\Breast cancer subtype\Basal
\Design Factors\Breast cancer subtype\Claudin-low
\Design Factors\Breast cancer subtype\Luminal
\Design Factors\Breast cancer subtype\Non-malignant
\Design Factors\Breast cancer subtype\unknown
2 tranSMART_test_RNAseq
tranSMART RC2 Release – Test Case (Working Document)
Tests
Step #
Instructions
Expected Results
Actual Results or Deviations/Comments
1
Go to the Analyze tab.
Heatmap generated.
Add Screenshot
Add comment:
Under Program ‘RC2 testing’, open the Study
'test_RNAseq’.
Drag and drop 'Design Factors/Breast cancer
subtype/Basal' as Subset 1.
Drag and drop 'Design Factors/Breast cancer
subtype/Luminal' as Subset 2.
Go to the ‘Advanced Workflow’ and select the ‘Heatmap’
analysis.
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
Click the ‘High Dimensional Data’ button and select the
pathway ‘Apoptosis’, and click ‘Apply Selections’.
Click the ‘Run’ button.
2
Under ‘Advanced Workflow’, select the ‘Heatmap’
analysis.
Heatmap generated.
Add Screenshot
Add comment:
Click OK on the pop up screen
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
3 tranSMART_test_RNAseq
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Step #
Instructions
Expected Results
Actual Results or Deviations/Comments
Heatmap generated.
Add Screenshot
Click the ‘High Dimensional Data’ button and click ‘Apply
Selections’.
Click the ‘Run’ button.
3
Under ‘Advanced Workflow’, select ‘Hierarchical
Clustering’ from the ‘Analysis’ drop down.
Add comment:
Click OK on the pop up screen
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
Click the ‘High Dimensional Data’ button and select the
pathway ‘Apoptosis’, and click ‘Apply Selections’.
Click the ‘Run’ button.
4
Under ‘Advanced Workflow’, select ‘K-Means Clustering’
from the ‘Analysis’ drop down.
Heatmap generated.
Add Screenshot
Add comment:
Click OK on the pop up screen
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
Click the ‘High Dimensional Data’ button and select the
pathway ‘Apoptosis’, and click ‘Apply Selections’.
Click the ‘Run’ button.
4 tranSMART_test_RNAseq
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Step #
Instructions
Expected Results
Actual Results or Deviations/Comments
5
Under ‘Advanced Workflow’, select ‘PCA’ from the
‘Analysis’ drop down.
Graph and tables
generated.
Add Screenshot
Add comment:
Click OK on the pop up screen.
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
Click the ‘High Dimensional Data’ button and select the
pathway ‘Apoptosis’, and click ‘Apply Selections’.
Click the ‘Run’ button.
6
Under ‘Advanced Workflow’, select ‘Marker Selection’
PCA’ from the ‘Analysis’ drop down.
Heatmap generated and
table.
Add Screenshot
Add comment:
Click OK on the pop up screen.
Drag and drop ‘Data/RNAseq/Breast’ under ‘Variable
Selection’.
Click the ‘High Dimensional Data’ button and select the
pathway ‘Apoptosis’, and click ‘Apply Selections’.
Click the ‘Run’ button.
7
Click on Comparaison tab and clear Subsets 1 and 2.
Drag and drop the Study ‘test_RNAseq’ as Subset 1.
5 tranSMART_test_RNAseq
Scatter Plot generated
with Linear Regression
Result table.
Add Screenshot
Add comment:
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Step #
Instructions
Expected Results
Actual Results or Deviations/Comments
...\Basal\
...\Claudin-low\
...\Luminal\
...\Non-malignant\
...\unknown\
appears in the box.
Add Screenshot
Under ‘Advanced Workflow’, select ‘Scatter Plot with
Linear Regression’ from the ‘Analysis’ drop down.
Drag and drop ‘Data/RNAseq/Breast’ in the ‘Independent
Variable’ box.
Click the ‘High Dimensional Data’ button and select the
gene ‘BAX’, and click ‘Apply Selections’.
Drag and drop ‘Data/RNAseq/Breast’ in the ‘Dependent
Variable’ box.
Click the ‘High Dimensional Data’ button and select the
gene ‘AIFM1’, and click ‘Apply Selections’.
Click the ‘Run’ button.
Click the ‘Download raw R data’ link. Save the
downloaded zip file. Open the folder and verify the
‘ScatterPlot’, the ‘Outputfile’ and the ‘LinearRegression’
files.
8
Under ‘Advanced Workflow’, select ‘Box Plot with
ANOVA’ from the ‘Analysis’ drop down.
Click OK on the pop up screen.
Drag and drop the node ‘Design Factors/Breast cancer
subtype’ in the ‘Independent Variable’ box.
Drag and drop ‘Data/RNAseq/Breast’ in the ‘Dependent
6 tranSMART_test_RNAseq
Box Plot generated and
ANOVA Result tables.
Add comment:
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Step #
Instructions
Expected Results
Actual Results or Deviations/Comments
Tables generated with
Fisher test.
Add Screenshot
Variable’ box.
Click the ‘High Dimensional Data’ button and select the
gene ‘BAX’, and click ‘Apply Selections’.
Click the ‘Run’ button.
9
Under ‘Advanced Workflow’, select ‘Table with Fisher
test’ from the ‘Analysis’ drop down.
Add comment:
Click OK on the pop up screen.
Drag and drop ‘Data/RNAseq/Breast’ in the ‘Independent
Variable’ box.
Click the ‘High Dimensional Data’ button and select the
gene ‘BAX’, and click ‘Apply Selections’.
Activate the checkbox ‘Enable binning’.
Activate ‘Bin the Independent Variable’.
Drag and drop the node ‘Design Factors/Breast cancer
subtype’ in the ‘Dependent Variable’ box.
Click the ‘Run’ button.
10
Go to the ‘Data Export’ and export low and high
dimensional data.
Export files generated.
Download the zip file and open the low and high data
Data contained in
7 tranSMART_test_RNAseq
Add Screenshot
Add comment:
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Step #
Instructions
Expected Results
files.
export files is consistent
with data contained in
‘R raw data’
downloaded file.
Verify all the low dimensional values.
Compare values for ‘BAX’ and ‘AIFM1’ with the values in
the Output file of the raw R data export.
8 tranSMART_test_RNAseq
Actual Results or Deviations/Comments
Pass/Fail/
Not Executed
tranSMART RC2 Release – Test Case (Working Document)
Screenshots
Step #1:
Step #2:
Step #3:
Step #4:
Step #5:
Step #6:
Step #7:
Step #8:
Step #9:
9 tranSMART_test_RNAseq
tranSMART RC2 Release – Test Case (Working Document)
Step #10:
10 tranSMART_test_RNAseq
tranSMART RC2 Release – Test Case (Working Document)
IV.
Test Summary
tranSMART instance
tranSMART_test_RNAseq_(empty)
Test case
< tranSMART URL >
Purpose
Analyze and export ‘RNA seq’ data using tranSMART
Function/Analysis
Pass
Fail
Not Executed
Executed By
Re-Execution Required?
Reviewed By
Open Issues
11 tranSMART_test_RNAseq
Deviation Summary
Date
Date