Thomas Funke wrote: > Hi all, > > I tried to do normalization of affymetrix data with bioconductor on a > Linux server. When I read in the cel files all seemed ok. But the next > step caused an error. With Win XP all works fine. Did anyone experience > similar problems? > > Thanks, > > Thomas
There is the Bioconductor mailing list for questions related to BioConductor. People on that list are more likely to be of help on related questions. Best, Uwe Ligges > > > > PI <- ReadAffy() > > PI > AffyBatch object > size of arrays=712x712 features (14 kb) > cdf=ATH1-121501 (??? affyids) > number of samples=6 > number of genes=506944 > annotation=ath1121501 > notes= Warning messages: > 1: Line starting '<TITLE>Error</TITLE> ...' is malformed! > 2: Line starting '<BODY> ...' is malformed! > 3: Line starting '<H1>Error</H1> ...' is malformed! > 4: missing cdf environment! in show(AffyBatch) > > > > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > other attached packages: > affy affyio Biobase > "1.14.0" "1.4.0" "1.14.0" > > > > ------------------------------------------------------------------------ > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.