genePattern data preprocessing

Created: 2010-05-24 22:42:38 Last updated: 2010-05-24 22:42:39

Download Workflow

preprocess data set using genePattern preProces service, the input <data /> should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default

preprocess data set using genePattern preProces service, the input <data /> should be in genePattern STATML format.

preprocess data set using genePattern preProces service, the input <data /> should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

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://www.myexperiment.org/workflows/964/download?version=2
[ More Info Expand ]

Workflow Components

Authors (2)

Titles (1)

Descriptions (3)

Dependencies (0)

Inputs (1)

Name	Description
rawData	the raw data element (<data/>) to be preprocessed. <data/> should be in STATML format.

Processors (18)

Name	Type	Description
dataXML	xmlsplitter
PreprocessDatasetParameterSetXML1	xmlsplitter
preProcessTestData	wsdl	Wsdl http://node255.broadinstitute.org:6060/wsrf/services/cagrid/PreprocessDatasetSTATMLService?wsdl Wsdl Operation performAnalysis
parametersXML12	xmlsplitter
parametersXML11	xmlsplitter
preprocessDatasetParameterSetXML	xmlsplitter
ceiling	stringconstant	Value 2.1
columnThreshold	stringconstant	Value 0.0
filterFlag	stringconstant	Value false
logBaseTwo	stringconstant	Value false
maxSigmaBinning	stringconstant	Value 1
minChange	stringconstant	Value 3.0
minDelta	stringconstant	Value 100.0
numberOfColumnsAboveThreshold	stringconstant	Value 1
numExclude	stringconstant	Value 0
preprocessingFlag	stringconstant	Value no-disc-or-norm
probabilityThreshold	stringconstant	Value 1.0
threshold	stringconstant	Value 20.0

Beanshells (0)

Outputs (1)

Name	Description
preProcessedData

Datalinks (19)

Source	Sink
rawData	dataXML:Data
threshold:value	PreprocessDatasetParameterSetXML1:threshold
numExclude:value	PreprocessDatasetParameterSetXML1:numExclude
preprocessingFlag:value	PreprocessDatasetParameterSetXML1:preprocessingFlag
logBaseTwo:value	PreprocessDatasetParameterSetXML1:logBaseTwo
filterFlag:value	PreprocessDatasetParameterSetXML1:filterFlag
minDelta:value	PreprocessDatasetParameterSetXML1:minDelta
ceiling:value	PreprocessDatasetParameterSetXML1:ceiling
minChange:value	PreprocessDatasetParameterSetXML1:minChange
columnThreshold:value	PreprocessDatasetParameterSetXML1:columnThreshold
maxSigmaBinning:value	PreprocessDatasetParameterSetXML1:maxSigmaBinning
probabilityThreshold:value	PreprocessDatasetParameterSetXML1:probabilityThreshold
numberOfColumnsAboveThreshold:value	PreprocessDatasetParameterSetXML1:numberOfColumnsAboveThreshold
parametersXML11:output	preProcessTestData:parameters
preProcessTestData:parameters	parametersXML12:input
dataXML:output	parametersXML11:data
preprocessDatasetParameterSetXML:output	parametersXML11:preprocessDatasetParameterSet
PreprocessDatasetParameterSetXML1:output	preprocessDatasetParameterSetXML:PreprocessDatasetParameterSet
parametersXML12:Data	preProcessedData

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Wei Tan

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Wei Tan

Information Attributions (0)

(Workflows/Files)

None

Information Tags (5)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3637 viewings

1688 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

genePattern data preprocessing

Created by Wei Tan on Monday 23 November 2009 18:13:09 (UTC)
genePattern data preprocessing

Created by Wei Tan on Monday 24 May 2010 22:42:38 (UTC)

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 (2)

Taverna 2

Uploader

Wei Tan

Lymphoma type prediction based on microar... (7)

Download

Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.

Created: 2010-05-11 | Last updated: 2010-05-11

Credits: Wei Tan Ravi Stian Soiland-Reyes

Taverna 2

Uploader

Wei Tan

caArray (1)

Download

preprocess data before it is sent to any GenePattern services.

Created: 2010-08-14 | Last updated: 2010-08-14

Credits: Wei Tan

genePattern data preprocessing

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Value

Value

Value

Value

Value

Value

Value

Value

Value

Value

Value

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (2)