Hi Benilton, One thing I don't understand isf why 'oligo' didin't require me to install the .cdf file, but 'affy' required me to install the .cdf file. I am curious that how 'oligo' figure how where the correct .cdf file is and use it? Regards, Peng On Mon, Aug 10, 2009 at 5:25 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: > Dear Peng, > > I can speak for oligo and the annotation package used by it. > > The current release of oligo summarizes to the probeset level. The next > release of oligo and annotation packages will allow you to summarize to the > gene level. In your particular case, the count you'll get is roughly 35K. > > The updated packages have already been submitted to BioC and soon should > show up on the devel branch. > > Best wishes, > > b > > On Aug 10, 2009, at 6:39 PM, Peng Yu wrote: > >> Hi, >> >> I have run the two different R script to do RMA. Neither of them gives >> me any error messages. However, the RMA results are very >> different---they have very different number of lines. I don't know >> which one I should believe. Or neither of them is correct. It might be >> due to the difference in the cdf file used. Would you please point to >> me how to figure out the problem? >> >> $ Rscript probe2expr_affy.R >>> >>> library(affy) >> >> Loading required package: Biobase >> Loading required package: methods >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >>> Data <- ReadAffy() >>> eset <- rma(Data) >> >> Background correcting >> Normalizing >> Calculating Expression >>> >>> write.exprs(eset, file="gene_expr_affy.txt", sep="\t") >>> >> >> $ Rscript probe2expr_oligo.R >>> >>> library(oligo) >> >> Loading required package: oligoClasses >> Loading required package: Biobase >> Loading required package: methods >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: preprocessCore >> Welcome to oligo version 1.8.1 >>> >>> data<-read.celfiles(list.celfiles()) >> >> Loading required package: pd.mogene.1.0.st.v1 >> Loading required package: RSQLite >> Loading required package: DBI >> Platform design info loaded. >> Reading in : koA-mth_HZ_5238_MST1_19389.cel >> Reading in : koB-mth_HZ_5238_MST1_19390.cel >> Reading in : koC-mth_HZ_5238_MST1_19391.cel >> Reading in : koD-mth_HZ_5238_MST1_19392.cel >> Reading in : wt1-mth_HZ_5238_MST1_19385.cel >> Reading in : wt2-mth_HZ_5238_MST1_19386.cel >> Reading in : wt3-mth_HZ_5238_MST1_19387.cel >> Reading in : wt4-mth_HZ_5238_MST1_19388.cel >>> >>> eset<-rma(data) >> >> Background correcting >> Normalizing >> Calculating Expression >>> >>> write.exprs(eset, file="gene_expr_oligo.txt", sep="\t") >>> >> >> $ wc gene_expr_affy.txt gene_expr_oligo.txt >> ?34761 ? 312848 ?5002519 gene_expr_affy.txt >> 234591 ?2111318 33763075 gene_expr_oligo.txt >> 269352 ?2424166 38765594 total >> >> BTW, before I run 'Rscript probe2expr_affy.R'. I downloaded >> MoGene-1_0-st-v1.r3.unsupported-cdf and I run the following script. >> Then, I install the generated package 'mogene10stv1cdf'. >> $ cat make_cdf_package.R >> library(makecdfenv) >> make.cdf.package("MoGene-1_0-st-v1.r3.cdf", >> packagename="mogene10stv1cdf", species="Mus_musculus") >> >> Regards, >> Peng >> >> _______________________________________________ >> 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 > >