TCGA.Merge

 TCGA.Merge - version 1

 

24 October 2011 - Robert Borkowski, robert.borkowski@utsouthwestern.edu

twitter: @rborkows

 

A module for collating TCGA Level 3 expression data, distributed in a one-file-per-sample format to a single, tab-delimited file with one probe per row, and one column per sample.

 

Be sure to check for proper line endings! Use the RXCtoGCT module to transform the output into a full-fledged .gct file.

 

Parameters: 

 

“input”: An archive (tested with .zip) containing BOTH the “file_manifest.txt” generated by TCGA during the data download, and each of the sample files you wish to collate.

 

“output”: The desired output file name. Will have “.txt” appended.

 

Known issues:

 

-Leaves behind the uncompressed .txt files.

 

 

 

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Version Comment: v1\: Now works by extracting an archive with the file manifest and per sample files.
Created by: Robert Borkowski
Uploaded by: rborkows on Mon, 10/24/2011 - 12:04
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LSID: urn:lsid:8080.aplab.swmed.edu:genepatternmodules:5:2
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Replies to TCGA.Merge forum

Comment Title Author Post date
Error with TCGA.Merge k.wroblewski 11/24/2011
 i have the same problem, and fist2005 04/07/2013