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Identification of differential genes using t-tests by R

Workflow Entry: Identification of differential genes using t-tests by R

Created at: 15/04/08 @ 15:37:42 Last updated: 01/07/08 @ 17:21:18

Version 2 (latest) (of 2)

Version created on: 15/04/08 @ 15:37:42 by: Peter Li | Revision comments Expand

Last edited on: 01/07/08 @ 17:21:18 by: Peter Li

Title: Identification of differential genes using t-tests by R

Type: Taverna 1

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Description

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

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Workflow Components

Inputs (0)

Processors (20)

Name	Type	Description
Ttest_pvalue	stringconstant
GoTermFinder_pvalue	stringconstant
getNamesUsingXPath	local	Parses the measurement names of microarray datasets from the XML output from maxdBrowse
flatten	local	Removes a layer of lists
performT_tests	rshell	This R script performs a series of t-tests for each gene expression level between its 2 input data sets.
mergeOutput1	beanshell	Merges the selected input data sets into a single data set
createFinalCSV	beanshell	Creates a text file in CSV format contain a list of the all the differentially expressed genes identified by the R script.
cleanCSV	beanshell	Removes unneccesary prefix text in the affy identifiers from the CSV file output generated by the R script
createGeneList	beanshell	Create a list of genes for analysis by the GOTermFinder service. Spurious genes are removed including those which have been annotated as questioable and hypothetical and therefore will not have a GO term asscoiated with them.
selectTestData	beanshell	Uses Java Swing classes to enable the user to select data sets for t-test analysis
getAffyIds	beanshell	Parses the affy identifiers from the CSV file
mergeOutput2	beanshell	Combines the selected data sets into a single data set
selectControlData	beanshell	Uses Java Swing classes to enable the user to select data sets for t-test analysis
getMeasurementNames	arbitrarywsdl	Querys the maxdload database using maxdBrowse to obtain a list of measurement names from the big experiment data stored there
queryMaxd1	arbitrarywsdl	Will take a list of Gene names, a list of Measurement names and a list of Column Types and produce a table. All values are coloured in relation to the a reference. In the list of Measurement names, the first Measurement listed is taken to be the reference. Formatted as text.
getGeneName	arbitrarywsdl	Gets the gene name for a given yeast open reading frame number
analyseGenesPDFOutput	arbitrarywsdl	Analyses a list of genenames using the GOTermFinder service
getTargetDescription	arbitrarywsdl	Gets a description of a given affy identifer using the YeastAffymapper service
getTranscriptId	arbitrarywsdl	Gets the open reading frame number for a given affy identifier
queryMaxd2	arbitrarywsdl	Will take a list of Gene names, a list of Measurement names and a list of Column Types and produce a table. All values are coloured in relation to the a reference. In the list of Measurement names, the first Measurement listed is taken to be the reference. Formatted as text.

Outputs (3)

Name	Description
pdf	A PDF document generated by the GoTermFinder service
csv	A text file in CSV format showing a list of differentially expressed genes and their annotations
spurious_genes	A text file in CSV format shoing a list of genes annotated as hypothetical, questionable, genomic sequences, etc. These genes do not have a GO term associated with them and so are removed from the list sent to the GoTermFinder service.

Links (28)

Sink	Source
analyseGenesPDFOutput:pvalue	GoTermFinder_pvalue:value
performT_tests:pvalue	Ttest_pvalue:value
flatten:inputlist	cleanCSV:out
analyseGenesPDFOutput:genes	createGeneList:orfs
spurious_genes	createGeneList:spurious_genes
createFinalCSV:affyIds	flatten:outputlist
getAffyIds:inList	flatten:outputlist
getGeneName:affyId	getAffyIds:outList
getTargetDescription:affyId	getAffyIds:outList
getTranscriptId:affyId	getAffyIds:outList
createFinalCSV:genenames	getGeneName:getGeneSymbolReturn
createGeneList:listOfGenenames	getGeneName:getGeneSymbolReturn
getNamesUsingXPath:xml-text	getMeasurementNames:return
selectControlData:input	getNamesUsingXPath:nodelist
selectTestData:input	getNamesUsingXPath:nodelist
createFinalCSV:descriptions	getTargetDescription:getTargetDescriptionReturn
createGeneList:listOfDescriptions	getTargetDescription:getTargetDescriptionReturn
createFinalCSV:orfs	getTranscriptId:getTranscriptIdReturn
createGeneList:listOfOrfs	getTranscriptId:getTranscriptIdReturn
performT_tests:control_csv	mergeOutput1:out
performT_tests:test_csv	mergeOutput2:out
cleanCSV:in	performT_tests:file
mergeOutput1:in	queryMaxd1:return
mergeOutput2:in	queryMaxd2:return
queryMaxd1:MeasurementNames	selectControlData:output
queryMaxd2:MeasurementNames	selectTestData:output
pdf	analyseGenesPDFOutput:analyseGenesPDFOutputReturn
csv	createFinalCSV:csv

Coordinations (1)

Controller	Target
mergeOutput1	selectTestData

Taverna 1 workflow

Information Original Uploader

Peter Li

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All versions of this Workflow are licensed under the Creative Commons Attribution-Share Alike 3.0 License.

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Peter Li

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Microarray data analysis using R
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Information Statistics

661 viewings

437 downloads

Citations (1)

1. Li, P., Castrillo, J. I., Velarde, G., Wassink, I., Soiland-Reyes, S., Owen, S., Withers, D., Oinn, T., Pocock, M. R., Goble, C. A., Oliver, S. G. & Kell, D. B., Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially expressed genes from microarray data, BMC Bioinformatics 2008, 9:334, 07 August 2008, http://www.biomedcentral.com/1471-2105/9/334

Version History

Earliest Version:
[1] - Identification of differentially-expressed genes using R

Created on: Tuesday 15 April 2008 @ 15:37:42 (BST)

Created by: Peter Li

Last edited on: Tuesday 15 April 2008 @ 15:41:25 (BST)

Last edited by: Peter Li

Revision comments:

None

Latest Version:
[2] - Identification of differential genes using t-tests by R

Created on: Tuesday 15 April 2008 @ 15:37:42 (BST)

Created by: Peter Li

Last edited on: Tuesday 01 July 2008 @ 17:21:18 (BST)

Last edited by: Peter Li

Revision comments:

Replaced the cleanGenenames processor with a new Beanshell script called createGeneNames. This new processor generates a list of genes using their yeast gene name or open reading frame number if it does not have a standard yeast name.