getAllQCProbes("ygs98cdf") produces the following vector of yeast control probes on the YG_S98 Affymetrix microarray chip: [1] "AFFX-YFL039C3_at" "AFFX-YFL039CM_at" "AFFX-YFL039C5_at" "AFFX- YER022w3_at" [5] "AFFX-YER022wM_at" "AFFX-YER022w5_at" "AFFX-YER148w3_at" "AFFX- YER148wM_a" [9] "AFFX-YER148w5_at" The 8th component of this vector is missing a 't' at the end. When I use simpleaffy with gc.affy(AffyBatch) I run into an error: Error in FUN(X[[8]], ...) : subscript out of bounds I traced this error to the eighth component of the qc vector above and the error occurs in the step: qc.probe.vals <- rbind(c(), (sapply(qc.probenames, function(y) { x[y, ] In debug mode when I edit qc.probenames I don't get an error. Juerg Straubhaar Umass Med Worcester

Hi, There was a typo in the set up file - I've fixed in version 2.05 (which will appear in the devl branch shortly). In the meantime if you want to get under the bonnet, in the package directory for simpleaffy you'll find a directory: 'data', containing the file 'qc.probes.tab'. Third line from the bottom you'll find your probeset; you can fix it in there... Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Straubhaar, Juerg Sent: 03 December 2004 19:35 To: bioconductor@stat.math.ethz.ch Subject: [BioC] error in ygs98cdf environment? getAllQCProbes("ygs98cdf") produces the following vector of yeast control probes on the YG_S98 Affymetrix microarray chip: [1] "AFFX-YFL039C3_at" "AFFX-YFL039CM_at" "AFFX-YFL039C5_at" "AFFX-YER022w3_at" [5] "AFFX-YER022wM_at" "AFFX-YER022w5_at" "AFFX-YER148w3_at" "AFFX-YER148wM_a" [9] "AFFX-YER148w5_at" The 8th component of this vector is missing a 't' at the end. When I use simpleaffy with gc.affy(AffyBatch) I run into an error: Error in FUN(X[[8]], ...) : subscript out of bounds I traced this error to the eighth component of the qc vector above and the error occurs in the step: qc.probe.vals <- rbind(c(), (sapply(qc.probenames, function(y) { x[y, ] In debug mode when I edit qc.probenames I don't get an error. Juerg Straubhaar Umass Med Worcester _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}