Hi, I have GeneChip Rate gene 1.1 st array and for some reason cdf library is not available with these array. there's the following file instead *.clf (CEL Layout File): which indicates the location of each probe within the CERevision Date 20090608:L matrix *.pgf (Probe Group File): which indicates the groupings of probes into probesets. *.bgp (BackGround Probe file): The bgp files lists the probe IDs for the background probes for use with the PM-GCBG intensity method. *.ps (ProbeSet list file): This file lists a particular set of probesets. This file may be used to process only a specific subset of the chip or it may be used to call out a special set of probesets on the chip. *.mps (Meta ProbeSet file): This file is used for gene level analysis on WT-based Gene and Exon arrays. It lists probesets in the PGF file to be merged together to create a gene level probeset. I would like to know if there's a way to generate a cdf from the the file mentioned above ? Thanks in advance . Kind Regards, Ramzi [[alternative HTML version deleted]]

If you use the oligo package, everything is already in place: http://www.bioconductor.org/packages/release/data/annotation/html/pd.r aex.1.0.st.v1.html with oligo, you'll be able to use RMA and get summaries at the probeset and gene levels: library(oligo) cels = list.celfiles() theData = read.celfiles(cels) probesetSumm = rma(theData, target="probeset") geneCoreSumm = rma(theData, target="core") geneExtendedSumm = rma(theData, target="extended") geneFullSumm = rma(theData, target="full") cheers, b On Mon, Jan 25, 2010 at 1:48 PM, Ramzi TEMANNI <ramzi.temanni at="" gmail.com=""> wrote: > Hi, > I have GeneChip Rate gene 1.1 st array and for some reason cdf library is > not available with these array. > there's the following file instead > *.clf (CEL Layout File): which indicates the location of each probe within > the CERevision Date 20090608:L matrix > *.pgf (Probe Group File): which indicates the groupings of probes into > probesets. > *.bgp (BackGround Probe file): The bgp files lists the probe IDs for the > background probes for use with the PM-GCBG intensity method. > *.ps (ProbeSet list file): This file lists a particular set of probesets. > This file may be used to process only a specific subset of the chip or it > may be used to call out a special set of probesets on the chip. > *.mps (Meta ProbeSet file): This file is used for gene level analysis on > WT-based Gene and Exon arrays. It lists probesets in the PGF file to be > merged together to create a gene level probeset. > I would like to know if there's a way to generate a cdf from the the file > mentioned above ? > > Thanks in advance . > > Kind Regards, > Ramzi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >