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

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