Hi Nicolas, On 3/21/2011 12:51 PM, Nicolas Servant wrote: > Thanks Jim. > I found a cdf on BrainArray > http://www.affymetrix.com/browse/products.jsp?navMode=34000&productI d=131554&navAction=jump&aId=productsNav#1_1 > Then I plan to simply use the RMA function from the affy package. > > require(hugene11stv1hsentrezgcdf) > require(hugene11stv1hsentrezg.db) > require(hugene11stv1hsentrezgprobe) > cdfname<- "hugene11stv1hsentrezg" > abatch<- ReadAffy(celfile.path=rawDataDir, cdfname=cdfname) > rmaData<- rma(abatch, cdfname = cdfname) > > Is there still some reason to use xps or oligo instead of the affy > package ? It depends on what you are trying to do. The MBNI re-mapped cdfs are nice because you get updated mappings, but for these chips the original mappings aren't that out of date. So I don't know how much you gain. In addition, AFAIK, the probes are collected into gene or transcript-level probesets, so you cannot do any exon-level analyses. Both oligo and xps will do RMA, but they also allow you to vary at what level you collapse the probes into probesets (exon or gene level). If you are interested in alternate splicing, then you might want to be able to do exon-level stuff. The downside of oligo and xps is that they take Affy at their word vis a vis the mapping of probes to (exons, transcripts), which involves mapping some probes to multiple things. This is a bit sketchy; by definition you don't know what those probes are measuring. The MBNI cdf packages have no multiple-mapped probes (they are discarded), so that isn't an issue. Best, Jim > The vignette of oligo seems to also use RMA ... > http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/d oc/V5ExonGene.pdf > > Thanks > Nicolas > > James W. MacDonald a ?crit : >> Hi Nicolas, >> >> On 3/21/2011 11:18 AM, Nicolas Servant wrote: >>> Hi, >>> >>> I'm looking for the cdf package of the Affymetrix Human Gene 1.1 ST >>> ArrayPlate. >>> I found the hugene1.0 package but not the 1.1 (only the annotation >>> package .db are available) ... >>> Does anybody know if such a package exists ? >> >> No. We build the cdf package for this chip (1.0) using the unsupported >> cdf file that affy supplies. They have never to my knowledge offered >> an unsupported version of the 1.1 chip, so we don't have a cdf package. >> >> You can however use some functions from the aroma.affymetrix project >> to create a cdf if you are feeling adventurous >> (https://stat.ethz.ch/pipermail/bioconductor/2010-December/036730.h tml). >> >> But you should really be using either oligo or xps to analyze these >> chips. The affy package was never intended for these chips, and there >> are real reasons not to use it. >> >> Best, >> >> Jim >> >> >>> >>> Thanks >>> Nicolas >>> >> > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Dear Nicolas, If you want to use xps for Gene 1.1 ST arrays depends on you. Some people consider it as an advantage that xps uses the official Affymetrix PGF-files and annotation files, and the fact that it allows to do the analysis on computers with 1-2 GB RAM only. Furthermore, xps does not only allow you to use RMA but also MAS5 for these arrays, and it supports DABG detection calls. 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 3/21/11 5:51 PM, Nicolas Servant wrote: > Thanks Jim. > I found a cdf on BrainArray > http://www.affymetrix.com/browse/products.jsp?navMode=34000&productI d=131554&navAction=jump&aId=productsNav#1_1 > Then I plan to simply use the RMA function from the affy package. > > require(hugene11stv1hsentrezgcdf) > require(hugene11stv1hsentrezg.db) > require(hugene11stv1hsentrezgprobe) > cdfname<- "hugene11stv1hsentrezg" > abatch<- ReadAffy(celfile.path=rawDataDir, cdfname=cdfname) > rmaData<- rma(abatch, cdfname = cdfname) > > Is there still some reason to use xps or oligo instead of the affy > package ? > The vignette of oligo seems to also use RMA ... > http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/d oc/V5ExonGene.pdf > > Thanks > Nicolas > > James W. MacDonald a ?crit : >> Hi Nicolas, >> >> On 3/21/2011 11:18 AM, Nicolas Servant wrote: >>> Hi, >>> >>> I'm looking for the cdf package of the Affymetrix Human Gene 1.1 ST >>> ArrayPlate. >>> I found the hugene1.0 package but not the 1.1 (only the annotation >>> package .db are available) ... >>> Does anybody know if such a package exists ? >> >> No. We build the cdf package for this chip (1.0) using the unsupported >> cdf file that affy supplies. They have never to my knowledge offered >> an unsupported version of the 1.1 chip, so we don't have a cdf package. >> >> You can however use some functions from the aroma.affymetrix project >> to create a cdf if you are feeling adventurous >> (https://stat.ethz.ch/pipermail/bioconductor/2010-December/036730.h tml). >> >> But you should really be using either oligo or xps to analyze these >> chips. The affy package was never intended for these chips, and there >> are real reasons not to use it. >> >> Best, >> >> Jim >> >> >>> >>> Thanks >>> Nicolas >>> >> > >