Dear Wolfgang, Thank you for your answer, I have already posted more information about my problem in response to another email: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 8224/match=error+if+is+int+totalPlate+argument+length+zero Please have a look at it. Thank you for pointing out that there is a newer version of limma, however the upgrade did not change anything. If you need more information please let me know. Kind Regards, Piotrek 2008/6/3 Wolfgang Huber <huber at="" ebi.ac.uk="">: > Dear Piotr, > > thank you for your report. I suppose that unless you supply (some of) the > .gpr files that cause your problem, and a more precise description of what > the problem is, it will be difficult to help you. > > Also, please use the latest release of R and limma. There will be more > common interest in discussing these than for obsolete versions. > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > Piotr St?pniak a ?crit 01/06/2008 23:33: >> >> Hello Everyone, >> >> I am having problems using limma to analyse my data. It seems that >> when executing the function read.maimages() over the data it gets read >> wrongly - the values are taken from first next to right column. So for >> example under "F543 >> Median" I get "F543 Mean" values and so on, this causes printer layout >> problem and any other function used on the data to fail... >> >> The function to read data looks like this: >> bialkoRaw<- read.maimages( dir(pattern="gpr"), columns=list(G="F543 >> Median", Gb="B543 Median", R="F633 Median", Rb="B633 Median"), >> annotation=c("Block", "Column", "Row", "Name", "ID"), row.names=NULL, >> stringsAsFactors = default.stringsAsFactors()) >> >> My sessionInfo(): >> >> R version 2.6.2 (2008-02-08) >> i486-pc-linux-gnu >> >> locale: >> C >> >> attached base packages: >> [1] grid splines tools stats graphics grDevices utils >> [8] datasets methods base >> >> other attached packages: >> [1] arrayQuality_1.18.0 gridBase_0.4-3 hexbin_1.14.0 >> [4] convert_1.16.0 RColorBrewer_1.0-2 cluster_1.11.10 >> [7] arrayMagic_1.16.1 genefilter_1.16.0 survival_2.34-1 >> [10] marray_1.18.0 vsn_3.6.0 affy_1.16.0 >> [13] preprocessCore_1.0.0 affyio_1.8.0 Biobase_1.16.3 >> [16] lattice_0.17-7 limma_2.14.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.0.6 DBI_0.2-4 RSQLite_0.6-8 >> [4] annotate_1.18.0 rcompgen_0.1-17 tcltk_2.6.2 >> >> >> Does anyone have any idea what might be wrong? >> I'd appreciate any help. >> >> Kind Regards, >> Piotr St?pniak >