Thanks! It worked! Best regards, Mikhail On Thu, Feb 14, 2013 at 3:35 PM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > getProbeInfo() has an argument called 'target', which (for Exon/Gene > ST arrays) is set by default to 'core'. > > Looks like you want to add this argument and set it to 'probeset'. > > probeInfo <- getProbeInfo(rawdata, c('fid', 'fsetid', 'atom', > 'transcript_cluster_id','exon_id'), target='probeset') > > Best wishes, b > > 2013/2/14 Mikhail Pachkov <pachkov at="" gmail.com="">: >> Dear All, >> >> I have got a strange problem. I try to get probe information >> (particularly I am interested in fsetid, fid, atom) with getProbeInfo >> function. Here is example: >> >> library(oligo); >> rawdata=read.celfiles("GSM529785.CEL.gz"); >> probeInfo <- getProbeInfo(rawdata, c('fid', 'fsetid', 'atom', >> 'transcript_cluster_id','exon_id')); >> >> However it looks like instead of fsetid function returns transcript_cluster_id: >> >>>probeInfo[1,] >> fid man_fsetid fsetid atom transcript_cluster_id exon >> 1 15 3029030 3029030 5132751 3029030 444853 >> >> If I check directly underlying database >> pd.huex.1.0.st.v2/extdata/pd.huex.1.0.st.v2.sqlite I can see that >> function returned transcript_cluster_id instead of fsetid. >> >>>select * from pmfeature where atom=5132751; >> fid|fsetid | atom | x | y >> 15|3029044|5132751|14|0 >> >> sqlite> select * from featureSet where fsetid=3029044; >> fsetid|strand|start|stop|transcript_cluster_id|exon_id|crosshyb_typ e|level|chrom|type >> 3029044|0|142991717|142991843|3029030|444853|1|1|9|1 >> >> Do I use wrong arguments for getProbeInfo? Is it bug? >> >> Thank you in advance! >> >> Best regards, >> >> Mikhail Pachkov >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor