Hi All, I am interested in using a reduced number of probe sets of HG- U133plus2, for example masking some probe sets, to run RMA for my data analysis. I guess that I should make all new .CEL files from the original data sets and a new .cdf file which is modified to fit my new data sets. I am wondering if there are some easy ways with BioC to achieve that? Do I have to write some codes with, e.g. Perl, to make the new data sets and a new cdf? Any suggestions and help will be greatly appreciated! JP Jin xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin@email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

At least as far as rma() goes you may supply a vector of probeset names using the subset argument. eg library(affy);library(affydata);data(Dilution) goodprobesets <- geneNames(Dilution)[1:10] eset <- rma(Dilution,subset=goodprobesets) eset On Tue, 2005-04-19 at 13:17 -0400, Jianping Jin wrote: > Hi All, > > I am interested in using a reduced number of probe sets of HG- U133plus2, > for example masking some probe sets, to run RMA for my data analysis. I > guess that I should make all new .CEL files from the original data sets and > a new .cdf file which is modified to fit my new data sets. I am wondering > if there are some easy ways with BioC to achieve that? Do I have to write > some codes with, e.g. Perl, to make the new data sets and a new cdf? > > Any suggestions and help will be greatly appreciated! > > JP Jin > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > x Jianping Jin Ph.D. x > x Bioinformatics scientist x > x Center for bioinformatics x > x 3133 Bioinformatics Building x > x CB# 7104 x > x University of North Carolina x > x Chapel Hill, NC 27599 x > x Tel: (919)843-6105 x > x Fax: (919)843-3103 x > x E-mail: jjin@email.unc.edu x > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor