[BioC] GEO + SOFT files

[Stephen Henderson]

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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