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! -- Bin Ye [[alternative HTML version deleted]]

Hi Bin, try to use lFarms in the farms package to process your arrays with loess normalization and farms summarization. Cheers, Okko -- dipl.-inf. djork clevert | gleimstr. 13a | d-10437 berlin e: okko at clevert.de p: +49.30.4432 4702 f: +49.30.6883 5307 Am 23.06.2011 um 14:55 schrieb Bin Ye: > 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! > > > -- > Bin Ye > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 Christian _._._._._._._._._._._._._._._._._._ 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! > >