Hi, In order to compare different types of affy chips, I construct manually AffyBatch object with NA values for the probes which are not in common. Unfortunately RMA doesn't deal with NA values. Is it possible to let the NA values during the normalization in the next release of RMA ? Or any kind of NA value management ? Thanks a lot -- Benjamin Haibe-Kains Licence in Computer Science Master in Bioinformatics Free University of Brussels (ULB) E-mail: bhaibeka@ulb.ac.be MicroArray Unity Institute Jules Bordet (IJB) E-mail: benjamin.haibekains@bordet.be

Benjamin Haibe-Kains wrote: > Hi, > > In order to compare different types of affy chips, I construct manually > AffyBatch object with NA values for the probes which are not in common. > Unfortunately RMA doesn't deal with NA values. Is it possible to let the > NA values during the normalization in the next release of RMA ? Or any > kind of NA value management ? Since you go for the creation of chimeric AffyBatch objects, what about creating an appropriate chimeric cdfenvs as well ? This means that only the probes you are interested in (i.e., non NA) are found such a cdfenv. (the packs altcdfenvs, makecdfenv, and matchprobes are likely contain code or examples or interest) L. > > Thanks a lot >

Did you look at the matchprobes package, which basically does this? There is a vignette which provides some details... On Mon, Oct 11, 2004 at 10:34:28AM +0200, Benjamin Haibe-Kains wrote: > Hi, > > In order to compare different types of affy chips, I construct manually > AffyBatch object with NA values for the probes which are not in common. > Unfortunately RMA doesn't deal with NA values. Is it possible to let the > NA values during the normalization in the next release of RMA ? Or any > kind of NA value management ? > > Thanks a lot > > -- > Benjamin Haibe-Kains > > Licence in Computer Science > Master in Bioinformatics > Free University of Brussels (ULB) > E-mail: bhaibeka@ulb.ac.be > > MicroArray Unity > Institute Jules Bordet (IJB) > E-mail: benjamin.haibekains@bordet.be > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+