Mayte, You don't need to send me a data object just your R script and your sessionInfo. Then I can try to reproduce the error you're getting. Matt On Sat, Apr 28, 2012 at 3:51 PM, Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> wrote: > Thanks Matthew, > > I am trying to preprocess two batches, hgu133a2 and hgu133plus2 separately using frma but I want to > then subset for the set of common probes, that's why I want to frma hgu133plus2 chips to hgu133a anyway, > I try the convertPlatform but as I said it did not work out. DO you me to send you ?affybatch ? > ?Txs > Mayte Suarez-Farinas > Research Assistant Professor, ?Laboratory of Investigative Dermatology > Biostatistician, ?Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178, > New York, NY, 10065 > Phone: +1(212) 327-8213 > Fax: ? ? ?+1(212) 327-8232 > > > > > > > > > > > On Apr 28, 2012, at 3:38 PM, Matthew McCall wrote: > >> Mayte, >> >> Do you mean you are trying to preprocess hgu133a2 and hgu133plus2 >> chips together? I wouldn't recommend this -- probe behavior (even for >> identical probes) seems to differ between the 2 platforms quite a bit. >> >> As for the hguXXXASXXFrma functions, these were replaced by >> convertPlatform (for the rare cases in which one might want to >> preprocess one platform as if it were really a different platform). >> This is mostly for special cases like hgu133atag and hgu133a, which >> differ by just a handful of probesets. >> >> If you provide an example (with sessionInfo), I can look into why >> convertPlatform might be failing. >> >> Best, >> Matt >> >> On Sat, Apr 28, 2012 at 9:28 AM, Mayte Suarez-Farinas >> <farinam at="" mail.rockefeller.edu=""> wrote: >>> Hi all, >>> >>> I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either ?functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result >>> >>> Error: could not find function "hgu133plus2ASaFrma" >>> >>> I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch) ?frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot. >>> >>> Thanks in advance!! >>> >>> Mayte Suarez-Farinas >>> Research Assistant Professor, ?Laboratory of Investigative Dermatology >>> Biostatistician, ?Center for Clinical and Translational Science >>> The Rockefeller University >>> 1230 York Ave, Box 178, >>> New York, NY, 10065 >>> Phone: +1(212) 327-8213 >>> Fax: ? ? ?+1(212) 327-8232 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> Matthew N McCall, PhD >> 112 Arvine Heights >> Rochester, NY 14611 >> Cell: 202-222-5880 > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880