Identification of differential genes using t-tests by R

Created: 2008-04-15 15:37:42 Last updated: 2008-07-01 17:21:18

Download Workflow

This workflow starts by retrieving the names of microarray datasets from the maxdLoad2 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 PDF file containing list of common GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

This workflow requires access to R deployed as a service using RServe for the RShell processor to run successfully.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/181/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (0)

Processors (20)

Name	Type	Description
flatten	local
performT_tests	rshell
getNamesUsingXPath	local
GoTermFinder_pvalue	stringconstant
Ttest_pvalue	stringconstant
getAffyIds	beanshell
mergeOutput2	beanshell
createFinalCSV	beanshell
cleanCSV	beanshell
selectControlData	beanshell
selectTestData	beanshell
cleanGenenames	beanshell
mergeOutput1	beanshell
getGeneName	arbitrarywsdl
getTargetDescription	arbitrarywsdl
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.
getMeasurementNames	arbitrarywsdl	Displays the measurement names for a database.
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.
getTranscriptId	arbitrarywsdl
analyseGenesPDFOutput	arbitrarywsdl

Beanshells (8)

Name	Inputs	Outputs
getAffyIds	inList	outList
mergeOutput2	in	out
createFinalCSV	affyIds orfs genenames descriptions	csv
cleanCSV	in	out
selectControlData	input	output
selectTestData	input	output
cleanGenenames	listofGenenames	genenames
mergeOutput1	in	out

Outputs (2)

Name	Description
pdf
csv

Links (25)

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

Coordinations (1)

Controller	Target
mergeOutput1	selectTestData

Information Workflow Type

Taverna 1

Information Uploader

Peter Li

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Peter Li

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (2)

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (2)

Information Statistics

4623 viewings

3240 downloads

[ see breakdown ]

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

In chronological order:

Identification of differentially-expressed genes using R

Created by Peter Li on Tuesday 15 April 2008 15:37:42 (UTC)

Last edited by Peter Li on Tuesday 15 April 2008 15:41:25 (UTC)
Identification of differential genes using t-tests by R

Created by Peter Li on Tuesday 15 April 2008 15:37:42 (UTC)

Last edited by Peter Li on Tuesday 01 July 2008 17:21:18 (UTC)

Revision comment:

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.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (3)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Peter Li

Identification of differential genes using... (1)

Download

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 which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

Created: 2008-07-02 | Last updated: 2008-07-02

Credits: Peter Li

Taverna 1

Uploader

Peter Li

Mapping microarray data onto metabolic pat... (1)

Download

This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: Peter Li