Dear Bioconductors,while re-running the basic rma protocol on some Affy mouse exon arrays (Mouse Exon 1.0 alias MoEx-1.0) I noticed that all at sudden I get 1201338 exons(/elements) instead of 1411189 in Oct 2007.  Since the R and the BioC release(s) changed, however, the annotation package (on www.bioconductor.org) is still the same (i.e. mouseexonpmcdf_1.1).a) Is this correct that mouse Affy exon 1.0 arrays now give just 1201338 exons ?b) How can one explain this change if the annotation underneith hasn't changed ?Here the code I use :library(exonmap)library(affy)dat.raw <- read.exon() dat.raw@cdfName <- "mouseexonpmcdf" eset.rma <- rma(dat.raw)  nrow(exprs(eset.rma)) # get (june 2008) : 1201338  ; BUT was (oct 2007) 1411189  eset.rma # gives :ExpressionSet (storageMode: lockedEnvironment)assayData: 1201338 features, 24 samples   element names: exprs phenoData sampleNames: A1xx.CEL, A2xx.CEL, ..., Z2xx.CEL  (24 total)  varLabels and varMetadata description:    sample: NA    treatment: NAfeatureData featureNames: 4304920, 4304921, ..., 5617580  (1201338 total) fvarLabels and fvarMetadata description: noneexperimentData: use 'experimentData(object)'Annotation: moex10stv1  sessionInfo()      # gives :R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale:Cattached base packages:[1] splines   tools     stats graphics  grDevices utils     datasets [8] methods   base     other attached packages: [1] mouseexonpmcdf_1.1   exonmap_1.6.02 plier_1.10.0         [4] RMySQL_0.6-0         DBI_0.2-4 RColorBrewer_1.0-2   [7] simpleaffy_2.14.05   gcrma_2.12.1 matchprobes_1.12.0  [10] genefilter_1.20.0    survival_2.34-1 affy_1.16.0         [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_2.0.1       loaded via a namespace (and not attached):[1] AnnotationDbi_1.0.6 RSQLite_0.6-8       annotate_1.18.0  Thanks for any helpful comments,Wolfgang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Wolfgang Raffelsberger, PhDLaboratoire de BioInformatique et Génomique IntégrativesIGBMC1 rue Laurent Fries, 67404 Illkirch  Strasbourg,  FranceTel (+33) 388 65 3300  ,      Fax (+33) 388 65 3276http://www-bio3d- igbmc.u-strasbg.fr/~wraffwolfgang.raffelsberger@igbmc.fr [[alternative HTML version deleted]]

Hi Wolfgang, I do not remember changing ever the CDFs for exon chips. 1411189 is the number of probesets for human chips. 1201338 is probably the right number for mouse. For rat it is some 1.1M So most likely you must have been running human CDF before... It is a bit like the joke (sorry, I could not help it ;) ): Teacher: ... and bear in mind that the boiling point for water is 90 degrees... Student: But professor, we were already told that the water boils in 100 degrees! T (checking his notes): Right, 90 degrees is the right angle... all the best, Michal Wolfgang RAFFELSBERGER wrote: > Dear Bioconductors,while re-running the basic rma protocol on some Affy mouse exon arrays (Mouse Exon 1.0 alias MoEx-1.0) I noticed that all at sudden I get 1201338 exons(/elements) instead of 1411189 in Oct 2007. Since the R and the BioC release(s) changed, however, the annotation package (on www.bioconductor.org) is still the same (i.e. mouseexonpmcdf_1.1).a) Is this correct that mouse Affy exon 1.0 arrays now give just 1201338 exons ?b) How can one explain this change if the annotation underneith hasn't changed ?Here the code I use :library(exonmap)library(affy)dat.raw <- read.exon() dat.raw at cdfName <- "mouseexonpmcdf" eset.rma <- rma(dat.raw) nrow(exprs(eset.rma)) # get (june 2008) : 1201338 ; BUT was (oct 2007) 1411189 eset.rma # gives :ExpressionSet (storageMode: lockedEnvironment)assayData: 1201338 features, 24 samples element names: exprs phenoData sampleNames: A1xx.CEL, A2xx.CEL, ..., Z2xx.CEL (24 total) varLabels and varMetadata description: sample: NA treatment: NAfeatureData featureNames: 4304920, 4304921, ..., 5617580 (1201338 total) fvarLabels and fvarMetadata description: noneexperimentData: use 'experimentData(object)'Annotation: moex10stv1 sessionInfo() # gives :R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale:Cattached base packages:[1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mouseexonpmcdf_1.1 exonmap_1.6.02 plier_1.10.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.14.05 gcrma_2.12.1 matchprobes_1.12.0 [10] genefilter_1.20.0 survival_2.34-1 affy_1.16.0 [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_2.0.1 loaded via a namespace (and not attached):[1] AnnotationDbi_1.0.6 RSQLite_0.6-8 annotate_1.18.0 Thanks for any helpful comments,Wolfgang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Wolfgang Raffelsberger, PhDLaboratoire de BioInformatique et G?nomique Int?grativesIGBMC1 rue Laurent Fries, 67404 Illkirch Strasbourg, FranceTel (+33) 388 65 3300 , Fax (+33) 388 65 3276http://www-bio3d- igbmc.u-strasbg.fr/~wraffwolfgang.raffelsberger at igbmc.fr > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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