[BioC] GEO + SOFT files

[Saurin D. Jani]

Hi,

You can go to this site below: Please read description of Method 14. Method 14
can analyze two-condition(Control vs Experimental , Wild Type vs Knock-Out,
Treatment 1 vs Treatment2 .. etc., ) GEO SOFT files with AFFY PLATFORM. There is
R script for that as well.

http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage&process=Methods_Library_List

That parser works for me for GEO SOFT file for AFFY data only. So, I don't know
if you have affy platform GEO SOFT files or no?

Saurin
 
-- 
|------------------------------------------------
| Saurin Jani,MS
| Statistical and Research Analyst
|
| Department of Cell Biology and Anatomy
| Medical  University of South Carolina (MUSC)
| 173 Ashley Ave
| Charleston,SC - 29407
| 
| Email: jani at musc.edu
| Phone: (843)792-1340
|------------------------------------------------


Quoting Stephen Henderson <s.henderson at ucl.ac.uk>:

> Hello
> I have found a number of references in the mailing list to dealing with SOFT
> files from the NCBIs GEO microarray database. One post was about a parser
> for SOFT files (see link)
> 
> http://files.protsuggest.org/biocond/html/7231.html
> 
> This sadly doesn't work for me (linux, Bioconductor1.6, R2.2). It hits an
> error and fails beyond the lines 
> 
> emX<- read.table(softFile, skip=Skpnum, comment.char="")
> Error in scan(file= file, what= what, sep =sep, quote= quote, dec =dec, :
> 	Line 22284 did not have 4 elements
> 
> 
> I suspect there are problems earlier too though. Has anyone else got this to
> work or made another parser (or better still a parser that is platform
> independent)?
> 
> 
> 
> Stephen Henderson
> Wolfson Inst. for Biomedical Research
> Cruciform Bldg., Gower Street
> University College London
> United Kingdom, WC1E 6BT
> +44 (0)207 679 6827
> 
> 
> 
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