[BioC] generate a CDF file from Affymetrix ST array 1.1 library

Benilton Carvalho beniltoncarvalho at gmail.com
Mon Jan 25 18:40:15 CET 2010

If you use the oligo package, everything is already in place:


with oligo, you'll be able to use RMA and get summaries at the
probeset and gene levels:

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")


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]]
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