Hi everybody! I'm a beginner in the analysis and interpretation of microarray data. I've been working with a Affymetrix's GeneChip? Rat Gene 1.0 ST Array and I have a doubt about the image that you get when using the command "image". There's two holes in the middle of the image, is this normal? Regards Germ?n -------------- next part -------------- A non-text attachment was scrubbed... Name: microarray.png Type: image/png Size: 23427 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090814="" b6fa4d90="" attachment.png="">

Hi everybody! I'm a beginner in the analysis and interpretation of microarray data. I've been working with a Affymetrix's GeneChip? Rat Gene 1.0 ST Array and I have a doubt about the image that you get when using the command "image". There's two holes in the middle of the image, is this normal? Regards Germ?n -------------- next part -------------- A non-text attachment was scrubbed... Name: microarray.png Type: image/png Size: 37711 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090813="" 9b212a46="" attachment.png="">

While I can not speak specifically about the Rat Gene Array. Such regions are typically control probe regions of one kind or another and found on most chips. Best, Ben On Fri, 2009-08-14 at 22:41 +0200, Germ?n Gonz?lez wrote: > Hi everybody! > > I'm a beginner in the analysis and interpretation of microarray data. I've been working with a Affymetrix's GeneChip? Rat Gene 1.0 ST Array and I have a doubt > about the image that you get when using the command "image". There's two holes in the middle of the image, is this normal? > > Regards > Germ?n > > _______________________________________________ > 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

(apologies in case my initial attempt of sending this message went through) Dear German, I apologize for the inconvenience this may have caused. The problem you reported is restricted to the image method. I'll submit the fix tonight and it'll be up, let's say, in about 2 days for download. In the meantime, if you want a temporary fix, please copy/paste the following code after loading oligo: setMethod("image", signature(x="FeatureSet"), function(x, which=0, transfo=log2, col=gray((0:64)/ 64), ...){ if (which == 0){ which <- 1:length(x) } if(length(which) > 1) par(ask=TRUE) else par(ask=FALSE) theDim <- geometry(getPD(x)) for (i in which){ tmp <- matrix(transfo(exprs(x[,i])), ncol=theDim[1], nrow=theDim[2]) tmp <- as.matrix(rev(as.data.frame(tmp))) image(tmp, col=col, main=sampleNames(x)[i], xaxt="n", yaxt="n", ...) } par(ask=FALSE) }) Thank you very much for your report, b On Aug 14, 2009, at 5:41 PM, Germ?n Gonz?lez wrote: > Hi everybody! > > I'm a beginner in the analysis and interpretation of microarray > data. I've been working with a Affymetrix's GeneChip? Rat Gene 1.0 > ST Array and I have a doubt > about the image that you get when using the command "image". There's > two holes in the middle of the image, is this normal? > > Regards > Germ?n > > <microarray.png><att00001.txt>

thanks Benilton and Ben. > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Argentina.1252;LC_CTYPE=Spanish_Argentina.1252;LC_M ONETARY=Spanish_Argentina.1252;LC_NUMERIC=C;LC_TIME=Spanish_Argentina. 1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.ragene.1.0.st.v1_2.4.1 RSQLite_0.7-1 [3] DBI_0.2-4 oligo_1.8.1 [5] preprocessCore_1.6.0 oligoClasses_1.6.0 [7] Biobase_2.4.1 loaded via a namespace (and not attached): [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.7 IRanges_1.2.3 [5] splines_2.9.0