Do we have any tools for parsing 1LQ files provided by Affymetrix? I know I can (in principle) use scan, but since the file in question is a little over 600MB, scan does not perform so well (meaning I killed it after a few hours). Preferably a binary tool like the stuff used by read.cdffile, read.affybatch /Kasper

Hi Kasper, I've just checked in an import function "getProbeData_1lq.R" for the makeProbePackage function in package matchprobes. It should be available on the bioC website in version 1.0.17 of the matchprobes package within a day or so. It does use the "scan" function though, and takes its time. (I found it more efficient to spend a little bit more of a computer's time doing this using a standard function, rather than my own time to write a parser in C - but the trade off may vary) Best wishes Wolfgang Kasper Daniel Hansen wrote: > Do we have any tools for parsing 1LQ files provided by Affymetrix? I > know I can (in principle) use scan, but since the file in question is a > little over 600MB, scan does not perform so well (meaning I killed it > after a few hours). Preferably a binary tool like the stuff used by > read.cdffile, read.affybatch > > /Kasper > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber