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 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

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 > > > > ********************************************************************** > This email and any files transmitted with it are confidentia...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >