[BioC] XPS package working with Affymetrix GeneChip 1.0 ST at gene level

[cstrato]

Dear Jorge,

You can preprocess both, RaExon and RaGene 1.0 ST arrays, at the 
probeset and the gene level, simply set the option to either 
option="probeset" or to option="transcript", e.g.:

data.rma <- rma(data.genome ,"RaGeneRMAMetacore", filedir=datdir 
background="antigenomic", normalize=TRUE, option="transcript", 
exonlevel="metacore+affx")

See the help file ?rma.

For further examples see the scripts "script4exon.R" and "script4xps.R" 
in the xps/examples directory. See also script "script4schemes.R" how to 
create the scheme for the RaGene array.

Best regards
Christian
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C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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On 6/2/12 3:02 AM, Jorge Miró [guest] wrote:
>
> I was wondering if there is some way of getting the XPS package working at gene level as I need to get the gene expression from some Rat Gene chips (RaGene 1.0 ST r4)that I will analyze.
>
> I tried to use the Affy package before but as far as I understand they need .CDF file to get working and I only have CLF and PBG files for my chips.
>
> Kind regards
> Jorge
>
>   -- output of sessionInfo():
>
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