Hi all, I am trying to load and apply some summarization methods to 200 .CEL files. The only R package I found solving this is aroma.affymetrix but it takes very long time to apply any normalization. I am using R 2.9 and aroma.affymetrix version 1.1.0. Is there any other solution to this problem, what do you ussally use? Thanks in advance. _________________________________________________________________ [[alternative HTML version deleted]]

Since you don't say what you've tried ("any normalization") and what you mean by "very long time", it's hard to know give details, but except from the fact that raw data is read from CEL file and normalized data is written back to another CEL file, there is nothing special in aroma.affymetrix that makes it slower than other methods. Actually great care has been taken to optimize algorithms/estimators for both memory and speed. What you might have experienced is the automatic generation of internal annotation files ("index files"), which happens once (in a lifetime) for each new chip type you analyze. You can read more about what is going on, here: http://groups.google.com/group/aroma-affymetrix/web/improving- processing-time [sorry for the current "spam-ban" hiccup by Google that you have to click through; very annoying] Henrik (author) 2009/6/16 UsuarioR Espa?a <kurtney_84 at="" hotmail.com="">: > > Hi all, > > I am trying to load and apply some summarization methods to 200 .CEL files. The only R package I found solving this is aroma.affymetrix but it takes very long time to apply any normalization. > > I am using R 2.9 and aroma.affymetrix version 1.1.0. > > Is there any other solution to this problem, what do you ussally use? > > Thanks in advance. > > > _________________________________________________________________ > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Dear Usuario Another option could be package xps available from BioC, see also: http://www.bioconductor.org/docs/workflows/oligoarrays/ 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 _._._._._._._._._._._._._._._._._._ UsuarioR Espa?a wrote: > Hi all, > > I am trying to load and apply some summarization methods to 200 .CEL files. The only R package I found solving this is aroma.affymetrix but it takes very long time to apply any normalization. > > I am using R 2.9 and aroma.affymetrix version 1.1.0. > > Is there any other solution to this problem, what do you ussally use? > > Thanks in advance. > > > _________________________________________________________________ > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >