AffyDEGFinder

186

Service version1.0

WSDL URLhttp://chipster.csc.fi/ws/chipster?wsdl PASSED

Given Affymetrix CEL files, AffyDEGfinder finds differentially expressed genes and runs clustering, annotation, and GO and KEGG enrichment analysis for them using R/Bioconductor through Chipster. This workflow consists of the following steps:

Normalize the data using rma (normalized.tsv)
Run a statistical test on the normalized data using empirical bayes (two-sample.tsv)
Perform hierarchical clustering (hc-genes.txt, hc-chips.txt)
Write out a heatmap image (heatmap.png)
Annotate results (annotations.tsv)
Run the term enrichment analysis for KEGG and GO pathways (hypergeo.html)

A description of the WSDL service:

Chipster

Namespace: http://chipster.csc.fi/chipster

Port: ChipsterPort
Location: http://chipster.csc.fi:80/chipster-ws/chipster
Protocol: http://schemas.xmlsoap.org/soap/http
Default Style: document

Operations

AffyDEGFinder

SOAP Action: http://www.csc.fi/chipster/AffyDEGFinder
Input Message: AffyDEGFinder
- parameters
  - AffyDEGFinder type AffyDEGFinderRequest
    - groups type GroupType
      - files type FileType
        name type string
        contents type base64Binary
        url type string
Output Message: AffyDEGFinderResponse
- parameters
  - AffyDEGFinderResponse type AffyDEGFinderResponse
    - normalizedData type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - deg type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - geneClustering type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - chipClustering type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - heatmap type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - annotations type FileType
      - name type string
      - contents type base64Binary
      - url type string
    - termEnrichmentAnalysis type FileType
      - name type string
      - contents type base64Binary
      - url type string

WSDL Changes

Date	Description of Changes
8th April 2009	First Snapshot

Test #1: AffyDEGFinder Java test

Run AffyDEGFinder for some kidney files using Java and JAX-WS RI.

Submitted by taavi on Wed, 11/19/2008 - 07:25

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