Thank you for pointing that out. I'm not sure how I caused that behavior. The important point is that I somehow caused it and it is not a problem with the way the get command works. That's a relief. I am still trying to diagnose a problem with some code. I think the nature of the problem is that when I remove all but one probe in a set from the cdf file then I am left with something that looks something like this: > a<-get("1552287_s_at", env=get(cdfpackagename)) > a pm mm 379214 380378 So there are no row numbers in this case, and I believe it is affecting my downstream code because the indices are lacking a dimension. Like this: some_pmIndex <- indexProbes(newAB,which="pm",genenames="1552287_s_at")[[1]] Error in ans[[i]][, i.probes] : incorrect number of dimensions I'll do some more testing to confirm the problem. Any ideas would be appreciated. Thanks for your patience. -Donna ----- Original Message ----- From: "James W. MacDonald" <jmacdon@med.umich.edu> Date: Wednesday, November 21, 2007 9:53 am Subject: Re: [BioC] getting the pm and mm indices To: Donna Toleno <toleno at="" usc.edu=""> Cc: bioconductor at stat.math.ethz.ch > I don't see that: > > > library(hgu133plus2cdf) > > Attaching package: 'hgu133plus2cdf' > > > get("1053_at", hgu133plus2cdf) > pm mm > [1,] 1193929 1195093 > [2,] 48229 49393 > [3,] 1014367 1015531 > [4,] 1076821 1077985 > [5,] 975016 976180 > [6,] 201506 202670 > [7,] 895292 896456 > [8,] 1170808 1171972 > [9,] 81075 82239 > [10,] 134485 135649 > [11,] 714108 715272 > [12,] 956498 957662 > [13,] 429738 430902 > [14,] 62512 63676 > [15,] 462278 463442 > [16,] 276396 277560 > > get("241053_at", hgu133plus2cdf) > pm mm > [1,] 620561 621725 > [2,] 1151233 1152397 > [3,] 477004 478168 > [4,] 742568 743732 > [5,] 930540 931704 > [6,] 288662 289826 > [7,] 255492 256656 > [8,] 623319 624483 > [9,] 1172293 1173457 > [10,] 11589 12753 > [11,] 1000379 1001543 > > indexProbes(dat, "pm")["1053_at"] > $`1053_at` > [1] 1193929 48229 1014367 1076821 975016 201506 895292 > 1170808 > 81075 > [10] 134485 714108 956498 429738 62512 462278 276396 > > indexProbes(dat, "pm")["241053_at"] > $`241053_at` > [1] 620561 1151233 477004 742568 930540 288662 255492 > 623319 > 1172293 > [10] 11589 1000379 > > > sessionInfo() > R version 2.6.0 beta (2007-09-24 r42966) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices datasets utils > methods[8] base > > other attached packages: > [1] hgu133plus2cdf_1.17.0 affy_1.16.0 preprocessCore_1.0.0 > [4] affyio_1.6.0 Biobase_1.16.0 rcompgen_0.1-15 > > Best, > > Jim > > > > Donna Toleno wrote: > > Hello Bioconductor list, > > > > I am using the "hgu133plus2cdf" as my cdfpackagename > > and I notice that I have a problem with the following commands > when a probe name is nested within other probenames. > > > > There is a probe named "1053_at" and "241053_at" > > > > For example, > > > >> a <- get("1053_at", env=get(cdfpackagename)) > >> a > > pm mm > > NA NA > > > > > >> indexProbes(mydata, "pm")["1053_at"] > > $`1053_at` > > pm mm > > NA NA > > > >> indexProbes(mydata, "pm")["1007_s_at"] > > $`1007_s_at` > > [1] 369707 563318 1049349 238813 1140401 1130782 1144961 > 207148 1144717 285805 1351879 1170814 906807 > > [14] 547053 1221909 2761 > > > > is the getProbeDataAffy a potential solution? > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >