Hello list, While checking my scripts against the new R/BioC versions, I encountered the following unexpected behaviour. Please consider the following peace of code: library(simpleaffy) x <- ReadAffy() > x AffyBatch object size of arrays=1002x1002 features (14 kb) cdf=Mouse430_2 (45101 affyids) number of samples=6 number of genes=1004004 annotation=mouse4302 notes= > featureNames(x)[1:5] [1] "1" "2" "3" "4" "5" > geneNames(x)[1:5] [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" ADDITIONALLY: when I do the following, the output is correct: x.norm <- rma(x) > featureNames(x.norm)[1:5] [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" > geneNames(x.norm)[1:5] [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" Warning message: 'geneNames' is deprecated. Use 'featureNames' instead. See help("Deprecated") Because of the "deprecated" message, I changed all geneNames() commands in featureNames() commands and hence found this inconsistency. I guess that my assumption is valid that the commands featureNames and geneNames should always obtain exactly the same results, is it not? If not, please explain! R/BioC is compiled and runnung on the following linux distribution: SUSE LINUX Enterprise Server 9 (x86_64) VERSION = 9 PATCHLEVEL = 3 The gcc version used is: gcc (GCC) 3.3.3 (SuSE Linux) Copyright (C) 2003 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Regards, Dr. Philip de Groot Wageningen University

Philip -- Thank you for the report. This has been corrected, and should appear as affy version 1.14.1 in the next couple of days. Martin "Groot, Philip de" <philip.degroot at="" wur.nl=""> writes: > Hello list, > > While checking my scripts against the new R/BioC versions, I encountered the following unexpected behaviour. Please consider the following peace of code: > > library(simpleaffy) > x <- ReadAffy() > >> x > AffyBatch object > size of arrays=1002x1002 features (14 kb) > cdf=Mouse430_2 (45101 affyids) > number of samples=6 > number of genes=1004004 > annotation=mouse4302 > notes= > >> featureNames(x)[1:5] > [1] "1" "2" "3" "4" "5" > >> geneNames(x)[1:5] > [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" > > ADDITIONALLY: when I do the following, the output is correct: > > x.norm <- rma(x) > >> featureNames(x.norm)[1:5] > [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" >> geneNames(x.norm)[1:5] > [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" > Warning message: > 'geneNames' is deprecated. > Use 'featureNames' instead. > See help("Deprecated") > > > Because of the "deprecated" message, I changed all geneNames() commands in featureNames() commands and hence found this inconsistency. I guess that my assumption is valid that the commands featureNames and geneNames should always obtain exactly the same results, is it not? > If not, please explain! > > R/BioC is compiled and runnung on the following linux distribution: > SUSE LINUX Enterprise Server 9 (x86_64) > VERSION = 9 > PATCHLEVEL = 3 > > The gcc version used is: > gcc (GCC) 3.3.3 (SuSE Linux) > Copyright (C) 2003 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > Regards, > > Dr. Philip de Groot > Wageningen University > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org