[BioC] Affymetrix Gene Chip Normalization

cstrato cstrato at aon.at
Thu Jun 23 17:32:23 CEST 2011

Dear Bin Ye,

Although xps does not support loess, it does support lowess and supsmu. 
See vignette xpsPreprocess.pdf (chapters 4 and 6).

Best regards
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

On 6/23/11 2:55 PM, Bin Ye wrote:
> Hi everyone,
> We had been working on analyzing some Affymetrix gene chip data (mogene 1.0
> st and hugene 1.0 st), and saw quite a few chips with intensity-dependent
> bias. These chips, after rma normalization using package oligo, give s-shape
> MA plots. We've tried xps package as well, but it doesn't seem to have loess
> normalization implemented for Affy GeneChip.
> So we're wondering if there's other packages/functions that can normalize
> Affymetrix gene chips using other methods, such as loess?
> Thanks in advance!

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