Hello Everyone, I am Piotr St?pniak, B.Sc. in Biotechnology, currently under M.Sc. course at Adam Mickiewicz University in Pozna?, Poland. I am working in Polish Science Academy in microarray experiments group. I'm a newbie in R and BioC, so please forgive me if my question is easy... I'm having problem with data import to RGList or marrayRaw objects. Using the following instruction: 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) The data seems to load, but $genes table looks odd, I guess the column names are shifted right by 1 column: $genes Block Column Row Name ID 1 1 1 ERG_Operon 2078 2647 2 2 1 ERG_Operon 2078 3102 3 3 1 ERG_Operon 2078 3549 4 4 1 FLT3_Operon 2322 3994 5 5 1 FLT3_Operon 2322 4444 2635 more rows ... This I think causes printer layout to be imported wrongly and then any other try to process the data (e.g. quality tests) produce such error message: Error in if is.int(totalPlate)) { : argument is of length zero The data is obtained with ScanArrayExpress software, so I have it in gpr or csv files, both give similar errors, but loading csv files seems also to fail import values for each channel and gets only the file name headers. Marray import also fails, I will skip the info about it not to enlarge the mail unnecessarily. My R session info is as follows: > 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 limma_2.14.1 [13] affy_1.16.0 preprocessCore_1.0.0 affyio_1.8.0 [16] Biobase_1.16.3 lattice_0.17-7 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 I think I should also say that these data causes import problems to any other data analysis software :( I also tried to read the printer layout from gal file, but all I got was "Block, Row, Column, ID columns not found" error. I'd greatly appreciate any help, please. Yours faithfully, Piotr St?pniak