Dear Mark, I built the package myself, because the decimal separator is different in our Illumina data files (see code attached). I will not accept any Illumina software background correction. I am using gcc version 4.1.2 with "-fpic -march=pentium4 -O3 -pipe -std=gnu99" Here my sessionInfo: R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: C attached base packages: [1] "grid" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.5.3" "1.2.0" "1.0.0" "1.1" "4.05" "0.72" affy affyio geneplotter lattice annotate Biobase "1.14.0" "1.2.0" "1.14.0" "0.15-4" "1.14.1" "1.14.0" limma "2.10.4" Thanks, Felix. Mark Dunning wrote: > Hi Felix, > > Could you tell me more about the system you are running please? If you > run the function sessionInfo() it will say which version of the package > you are using, the version of R and operating system. Did you download a > compiled version of the package or did you build it from the source code > on your own machine? I suspect that this is a C compiler issue, but I > need more information to be sure. > > Regards, > > Mark > > PS if you set useImages = FALSE in readIllumina, it will read the > background corrected values found in the text files and skip the image > processing steps. This will speed up the process of reading the raw data > (if you are willing to accept what Illumina do for background correction!). > > > On 13 Jun 2007, at 16:00, Felix Engel wrote: > >> Dear Mark Dunning. >> >> With the latest SVN version of beadarray the background-read problem >> (raw data import) remains, when issuing: >> >> BLData = readIllumina(imageManipulation = "none", >> backgroundMethod="none", textType=".txt") >> >> I still cannot explain resulting background values below zero: There are >> 500000 beads with average intensity -215359277, where another 500000 >> beads on the array give a normal background (average intensity 630). >> >> Thanks for your insight, >> >> Felix. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: readIllumina.R Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070614/ 8c5301db/attachment.pl