Yi: Could you send the output of sessionInfo() to the list? I am attaching mine at the end. I guess that you are using an old version of limma (when field dimensions had only one block). It is recommended to upgrade to a more recent version (e.g., 2.10.5). > so read.imagene() calculates the total number of spots as prod(FD): > nspots <- prod(FD) Y <- matrix(0, nspots, narrays) Looking at the actual code of read.imagene gives nspots <- sum(apply(FD, 1, prod)) which seems good enough to handle your situation. Best, Saroj ------------------------------- > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: limma "2.10.5" -------------------------------- > On Thu, June 28, 2007 5:33 pm, Yi Xing wrote: > Hello Saroj, > > > Thanks for your message. I think the problem is with the Field > Dimensions. It looks like this for my file: > > > Field Metarows Metacols Rows Cols > Block1 1 1 15 14 > Block2 1 1 15 14 > Block3 1 1 15 14 > Block4 1 1 15 14 > Block5 1 1 15 14 > Block6 1 1 15 14 > Block7 1 1 15 14 > Block8 1 1 15 14 > Block9 1 1 15 14 > Block10 1 1 15 14 > Block11 1 1 15 14 > Block12 1 1 15 14 > Block13 1 1 15 14 > Block14 1 1 15 14 > Block15 1 1 15 14 > Block16 1 1 15 14 > Block17 1 1 15 14 > Block18 1 1 15 14 > Block19 1 1 15 14 > Block20 1 1 15 14 > Block21 1 1 15 14 > Block22 1 1 15 14 > Block23 1 1 15 14 > Block24 1 1 15 14 > Block25 1 1 15 14 > Block26 1 1 15 14 > Block27 1 1 15 14 > Block28 1 1 15 14 > Block29 1 1 15 14 > Block30 1 1 15 14 > Block31 1 1 15 14 > Block32 1 1 15 14 > > > > which is 2.046527e+74, causing the error in the next line. > > Yi > On Jun 28, 2007, at 2:21 PM, Saroj Mohapatra wrote: > > >> Hello Yi, >> >> >> It is possible that there is a discrepancy between the number of spots >> calculated from the Field Dimensions in header and the number of rows it >> actually reads from the file. >> >> For example, in my Imagene 5.1 file: >> in the header, below "Begin Field Dimensions" I find the following: >> Metarows = 8 >> Metacols = 4 >> Rows = 15 >> Cols = 12 >> >> >> So, the total number of spots = 5760 >> In the data section of my file, there are 5760 rows (excluding column >> titles). >> >> Of course, the actual number would vary, you would have a different >> number of spots. You could start with checking that the numbers match. >> >> Also, there should be something like "Begin Raw Data" before the first >> line and "End Raw Data" after the last line of data section. >> >> Good luck! >> >> >> Saroj >> >> >> Yi Xing wrote: >> >> >>> Hi, >>> >>> >>> I tried to read several Imagene files with LIMMA: >>> >>> >>> library(limma) targets<-readTargets() >>> files<-targets[,c("FileNameCy3","FileNameCy5")] >>> RG<-read.maimages(files,source='imagene') >>> >>> >>> however, I got this error message: >>> >>> Read header information >>> Error in matrix(0, nspots, narrays) : matrix: invalid 'nrow' value >>> (too large or NA) >>> In addition: Warning message: >>> NAs introduced by coercion >>> >>> >>> What might be the problem and how to fix it? Thanks. >>> >>> >>> Yi Xing >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >> <smohapat.vcf> >> >