Thank you for your answer. nrow( abatch ) returns 732 (as expected), but getOption("BioC")$affy$xy.offset returns 1 (instead of 0). Loaded libraries: affy version 1.4.32 and drosophila2cdf version 1.4.7 (in this order) Thanks again, Eric > Eric Blanc wrote: >> Dear List, >> >> I have problems understanding probe indices for the Drosophila2 chip: >> the xy2indices and xy2i functions return different values, and I >> couldn't find anywhere whether either of them has been deprecated. xy2i >> seems to return indices compatible with pmindex, mmindex and probeIndex >> functions. (I made sure that the indices from the functions pmindex, >> mmindex and indexProbes were self-consistent and they are. The MM index >> always is 732 greater than its corresponding PM index). >> >> Also, the number of indices returned by the pmindex, mmindex and >> probeIndex functions is 42 less than the number of probes in the >> drosophila2probe data frame. All probes from sets "AFFX-Dm- pd2EGFP_at", >> "AFFX-Dm-pAsRed2_at" and "AFFX-Dm-pDsRed-Exp_s_at" seem to be missing. >> I don't know why they don't come up, as they aren't those which have an >> even y coordinate (only 180 probes in 9 probesets or 20 probes each). >> >> So my questions are: >> >> 1) Can you confirm that xy2i and i2xy are indeed the functions to use >> instead of xy2indices and indices2xy ? > > These two functions should return the same thing. What do you get from > nrow(abatch), where abatch is the name of your AffyBatch? Also, what do > you get from getOption("BioC")$affy$xy.offset? > > For the first, you should get 732, and from the second you should get 0. > If so, the functions should return identical results. > > >> 2) Is there anything wrong with the 3 missing probe sets that I should >> know ? > > I don't think there is anything wrong with them - for whatever reason, > Affy did not include these three probes in the cdf for this chip, but > they did include them in the probe_fasta file, which is why you are > getting differences between the cdfenv and the probe package. > > Best, > > Jim > > >> >> >> platform powerpc-apple-darwin7.4.0 >> arch powerpc >> os darwin7.4.0 >> system powerpc, darwin7.4.0 >> status >> major 1 >> minor 9.1 >> year 2004 >> month 06 >> day 21 >> language R >> >> affy version 1.4.32 >> >> >> Thanks very much for your help, >> Eric >> >> -- >> Dr. Eric Blanc e-mail: eblanc at ebi.ac.uk >> European Bioinformatics Institute Tel: +44 +1223 492 537 >> Wellcome Trust Genome Campus Fax: +44 +1223 494 468 >> Hinxton - Cambridge CB10 1SD >> - UNITED KINGDOM - >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Dr. Eric Blanc e-mail: eblanc at ebi.ac.uk European Bioinformatics Institute Tel: +44 +1223 492 537 Wellcome Trust Genome Campus Fax: +44 +1223 494 468 Hinxton - Cambridge CB10 1SD - UNITED KINGDOM -