[BioC] RMA hist

[Delphine Fleury]

Dear all,
I analyse affymetrix data to compare transcripts between the wild-type
and 3 mutants. After normalization using the RMA method, the histogram
of distribution of exprs(eset) isn t normal (cf histesetDataRMA.ps). It
seems there two distributions in each array hist. If I continue the
analysis using lm.series, all genes are significant. I guess that it
remains a variation source which is not normalized. Do you have any idea
of what it could be and how I can remove this variation ?

The procedure I did:
> Data<-ReadAffy()
> eset<-rma(Data)
> fit<-lm.series(exprs(eset), d1)
> eb<-ebayes(fit)
> d1
             WT A B C
Exp143hyb246   1   0   0   0
Exp143hyb247   1   1   0   0
Exp143hyb248   1   0   1   0
Exp143hyb249   1   0   0   1
Exp143hyb410   1   0   0   0
Exp143hyb411   1   0   0   0
Exp143hyb412   1   1   0   0
Exp143hyb413   1   1   0   0
Exp143hyb414   1   0   1   0
Exp143hyb415   1   0   1   0
Exp143hyb416   1   0   0   1
Exp143hyb417   1   0   0   1
> toptable(coeff=2, number=22810, genelist=gnames,
fit=fit,eb=eb,adjust="fdr")

I tried also the MAS5 procedure to normalize but the histograms of
exprs(eset) is more far from the gaussian and all genes are also
signficant with the same linear model.

Thanks for your answers.
Delphine

--
==================================================================
Delphine Fleury
DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
mailto:defle at psb.ugent.be                  http://www.psb.ugent.be
==================================================================

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