Hi Wenqiong, Thanks for you suggestion. I haven't had much time to devote to this yet, but importing the txt file as you suggest below rather than a zip file still results in the same error you encountered: >>Error in rep.default(NA, max(pm1, mm1, pm2, mm2)) : >>invalid number of copies in "rep" >>In addition: Warning messages: >>1: NAs introduced by coercion >>2: NAs introduced by coercion >>3: NAs introduced by coercion As Wolfgang suggested, I may need to try a different function or find someone more knowledgeable than I about R processes. Did you have column headers that were different than the standard affy, e.g.: Probe Set Name, Probe X, Probe Y, Probe Interrogation Position, Probe Sequence, Target Strandedness? Best Regards, Nathan Salomonis -----Original Message----- From: Wenqiong Chen [mailto:wenchen@diversa.com] Sent: Thursday, September 01, 2005 3:16 PM To: Nathan Salomonis Cc: bioconductor at stat.math.ethz.ch; Wolfgang Huber Subject: RE: [BioC] Matchprobe package Hi, Nathan: I was the one who posted the message long time ago which you quoted in your message. This is the command I tried which worked eventually, which is, believe or not, much straightforward. > makeProbePackage("disdiv712a", datafile="diS_div712a_probeSequenceFile.txt", maintainer = "Joan Chen <jchen at="" diversa.com="">", version = "0.0.1", force=TRUE) Where you only need to supply unzipped txt file of your probe tab file. You do need to supply the column names in this txt file. Hope this also works for you! Best, ************************* Wenqiong J. Chen, Ph.D Bioinformatics Staff Scientist Diversa Corp. 4955 Directors Place SD, CA 92121 (O): (858)-526-5334 jchen at diversa.com ************************* -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wolfgang Huber Sent: Thursday, September 01, 2005 2:33 PM To: Nathan Salomonis; 'bioconductor at stat.math.ethz.ch' Subject: Re: [BioC] Matchprobe package Dear Nathan, please excuse the delayed reply. The answer is yes. You can import a wide variety of probe-description files by adapting the function which is given to the 'makeProbePackage' function by the 'importfun' parameter. Have a look at the default 'getProbeDataAffy', this is a function that works for the "normal" probe_tab files. Its (simple) commented source code is available through the source packages (.tar.gz). I recommend using this as a template and adapting it. You can use "options(error=recover)" and the debugging browser of R to see what exactly is going wrong with your file. I am afraid it is difficult to tell for me from the information you provide, and I suppose with a little bit of basic R knowledge (maybe ask a local guru) you should be able to trace this down. Best wishes Wolfgang > > I was having the same error as with the user in the thread below. I > have a custom Affymetrix array (non-commercial) that has no mis- match > probes only perfect match. I have generated a CDF file and run RMA > successfully. I have also generated a file analogous to the > _probe_tab files supplied by Affymetrix (except I didn't include a > Probe Interrogation Position since I didn't have consensus sequence > information - left all values for this column > zero) and compressed it in .gz format. Can I expect to be able to > generate a proper probe package given that there are no mismatch probes? > > > > Best Regards, > > Nathan > > > > > > >>Hi, >>I am trying to make probe package with the functions in the "matchprobe" >>package. However, we have modified the cdf file and probe sequence >>file to accommodate the recent update of the in house genome sequence. >>I have successfully created the cdf package with the modified cdf >>file, and everything worked as far as use rma. However, to get the >>GCRMA work I would need to create the probe package where I am having >>trouble. I have checked that all the probe sequences within the cdf >>file were included in the probe sequence file, although the probe >>sequence file contain more sequences than the ones in the cdf file. >>Here the error message I got: >> >> >> >>>library(matchprobes) >>>makeProbePackage("disdiv712a", getProbeDataAffy("disdiv712a", >> >>"diS_div712a_probeSequenceFile.txt", pkgname = NULL, comparewithcdf = >>TRUE), maintainer = "XXXX<xxxx at="" diversa.com=""> > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >", version = > "0.0.1", > >>force=TRUE) >>Error in rep.default(NA, max(pm1, mm1, pm2, mm2)) : >>invalid number of copies in "rep" >>In addition: Warning messages: >>1: NAs introduced by coercion >>2: NAs introduced by coercion >>3: NAs introduced by coercion >> >>Can anyone please point out what is wrong? >>Thanks in advance! >> >>wenqiong >> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ---------------------------------------------------------------------- ------ -- This email message and any attachments are confidential and ...{{dropped}}