Hi, I got the following error message "Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed" when I was trying galinfo<-read.Galfile("pg.gal"). Here is the link to the gal file: http://www.brop.org:8000/pg.gal Is there anything wrong with the pg.gal file? Thanks. Meng

Hi Meng-Chuan, what package, which version, which version of R, what platform are you using? I have seen similar errors from marray::readGalfile, they were an interaction between the "locale" (i.e. the way your operating system and/or R represents characters as bytes) and the way that that funtion is programmed. Hard to say more though without further details. Cheers Wolfgang Cheng, Meng-Chuan wrote: > Hi, > I got the following error message > > "Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed" > > when I was trying galinfo<-read.Galfile("pg.gal"). > Here is the link to the gal file: http://www.brop.org:8000/pg.gal > > Is there anything wrong with the pg.gal file? > > Thanks. > > Meng > > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

Meng-Chuan, On your gal file I can get the same error, this is because your gal file header information is >100 lines long. read.Galfile tries to automatically work out how many lines to skip before reading in any data. y <- readLines(f, n = 100) # only reads first 100 lines if (classinfo.id) == "character") skip <- intersect(grepinfo.id[1], y), greplayout.id[1], y))[1] - 1 else skip <- intersect(grep("ID", y), grep("Name", y))[1] - 1 So skip becomes an NA as it cant see the start of the row with "Name" in it, and read.table fails. There is a slight bug in the coding as read.Galfile allows an arguement for manual override of skip, galinfo <- read.Galfile("pg.gal", skip=103), but it gets overwritten by the if else statement and fails anyway... Quick fix is to change, y <- readLines(f, n = 100) to y <- readLines(f, n = 120) # anything greater than 102 in your copy of read.Galfile. Also, your gal file appears to be non standard, see example http://www.axon.com/gn_GenePix_File_Formats.html#gal, specifically Block Column Row nesting order (should be Column nested in Row nested in Block - yours is different). This can be an issue if relating genes from a galfile list to marrayRaw/marrayNorm intensity information when the nesting is not the same in the files which load the intensity information into the marrayRaw object. For GenePix gpr files, a way round this is to run read.Galfile on the first array (assuming the template is the same in the batch), reading in the gal information in the same row order as the intensities in the gpr file. Marcus packageDescription("marray", field="Version") [1] "1.5.25" > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 0.1 year 2004 month 11 day 15 language R > >>> Wolfgang Huber <huber@ebi.ac.uk> 13/05/2005 3:43:51 p.m. >>> Hi Meng-Chuan, what package, which version, which version of R, what platform are you using? I have seen similar errors from marray::readGalfile, they were an interaction between the "locale" (i.e. the way your operating system and/or R represents characters as bytes) and the way that that funtion is programmed. Hard to say more though without further details. Cheers Wolfgang Cheng, Meng-Chuan wrote: > Hi, > I got the following error message > > "Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed" > > when I was trying galinfo<-read.Galfile("pg.gal"). > Here is the link to the gal file: http://www.brop.org:8000/pg.gal > > Is there anything wrong with the pg.gal file? > > Thanks. > > Meng > > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}