Hi Benilton, Thanks for the note. What I intended to do is to get the intensity data from Affy SNP cel files and do copy number analysis. So for oligo, after snprma(), I can take the ave of the two strand and then accomplish what I said in the above? Best, Allen On Nov 9, 2007 11:29 PM, Benilton Carvalho <bcarvalh at="" jhsph.edu=""> wrote: > oligo doesn't "produce" data on both strands, per se. :-) > > The data are given on both strands, for some SNPs on the 500K array > set. If one uses snprma(), oligo *summarizes* these data to the > SNP-allele-strand level. > > It's a little bit hard to say what to do, when we don't know what it's > going to be used for... > > An ad-hoc method for summarization to the SNP-Allele level can be > achieved by taking the average log-intensities across strands; or one > can choose to manually run a summarization algorithm (say > median-polish) on the SNP-allele sets (a la RLMM). > > Cheers, > > b > > > On Nov 8, 2007, at 9:51 PM, affy snp wrote: > > > Hi Ben, > > > > I checked it out and found oligo would produce data for two strands, > > sense and anti-sense. > > Is there a way to somehow combine the two type of datawhich will make > > sense? > > > > Thank-you! > > > > Allen > > > > > > On 11/8/07, Benilton Carvalho <bcarvalh at="" jhsph.edu=""> wrote: check the > > oligo package, but you also need to download the data > >> packages for the arrays you're using: > >> > >> pd.mapping250k.sty > >> pd.mapping250k.nsp > >> > >> b > >> > >> On Nov 8, 2007, at 9:34 PM, affy snp wrote: > >> > >> > Dear list, > >> > > >> > I am analyzing a bag of Affy SNP 500K arrays and would like to > >> > know which package can be used to read in the raw .CEL files > >> > and get the intensity values. In other words, I am looking for > >> > the function like: > >> > > >> > library(affy) > >> > mydata <- ReadAffy() > >> > eset_rma <- rma(mydata) > >> > > >> > provided by affy package to analyze affy gene expression data. > >> > > >> > Thank you very much! > >> > > >> > Sincerely, > >> > Allen >