Hi there, I'm trying to do some qualitycheck on my microarray data. R seems to have a problem with the file. > data = readGPR(fnames = "1.1_Cy3_over_Cy5.gpr", path="/home/tom /microarray-experiment1_gpr_files/", DEBUG=TRUE) [1] "Starting readGPR" [1] "/home/tom/microarray-experiment1_gpr_files/" [1] NA [1] "Reading /home/tom/microarray- experiment1_gpr_files//1.1_Cy3_over_Cy5.gpr" Error in readLines(con, n, ok) : invalid value for 'n' In addition: Warning messages: 1: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 2: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 3: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 4: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 5: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 6: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 7: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 8: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 9: input string 32 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) > Does anybody now what's the problem here? Greetz, Tom

Hi Tom, you'll need to tell us more about your OS, your R version (the value of 'version'), your locale (e.g. the result of the shell command 'locale') and your compile-options (the last couple of lines of config.log) in order to make sense of your question. There was a similar thread not long ago, https://stat.ethz.ch/pipermail/bioconductor/2005-May/008927.html Perhaps it is also possible for the arrayQuality / marray people to make things more robust to this or have better error messages? Best wishe Wolfgang Koonen wrote: > Hi there, > > I'm trying to do some qualitycheck on my microarray data. R seems to > have a problem with the file. > > >>data = readGPR(fnames = "1.1_Cy3_over_Cy5.gpr", path="/home/tom /microarray-experiment1_gpr_files/", DEBUG=TRUE) > > [1] "Starting readGPR" > [1] "/home/tom/microarray-experiment1_gpr_files/" > [1] NA > [1] "Reading /home/tom/microarray- experiment1_gpr_files//1.1_Cy3_over_Cy5.gpr" > Error in readLines(con, n, ok) : invalid value for 'n' > In addition: Warning messages: > 1: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 2: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 3: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 4: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 5: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 6: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 7: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 8: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 9: input string 32 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > > > Does anybody now what's the problem here? > > Greetz, Tom > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- 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

Tom, Try > library(limma) > readGPRHeader("/home/tom/microarray- experiment1_gpr_files/1.1_Cy3_over_Cy5.gpr")$NHeaderRecords This will tell you whether the GPR file header is valid and how long it is. Gordon >[BioC] readGPR (arrayQuality) >Paquet, Agnes apaquet at medsfgh.ucsf.edu >Tue Jun 28 00:54:43 CEST 2005 > >Hi Tom, > >readGPR is searching for the column named "F635 Median" in the gpr file >to determine which line contains the headers. The search is limited to >the first 100 lines. For some reasons, the function didn't find this >column name in the first 100 lines, probably because your header is >longer that 100 lines. One way around it is to open your gpr file in >excel, count manually how many lines are in your header and set the skip >argument to this number. > >If your header is less than 100 lines and your file has a column named >"F635 Median", could you please send me an example of the gpr files you >are using so that I can reproduce and fix this problem? > >Best, > >Agnes > >-----Original Message----- >From: bioconductor-bounces at stat.math.ethz.ch >[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Tom Koonen >Sent: Monday, June 27, 2005 2:24 PM >To: bioconductor at stat.math.ethz.ch >Subject: [BioC] readGPR (arrayQuality) > >Hi there, > >I'm trying to do some qualitycheck on my microarray data. R seems to >have a problem with the file. > > > data = readGPR(fnames = "1.1_Cy3_over_Cy5.gpr", >path="/home/tom/microarray-experiment1_gpr_files/", DEBUG=TRUE) >[1] "Starting readGPR" >[1] "/home/tom/microarray-experiment1_gpr_files/" >[1] NA >[1] "Reading >/home/tom/microarray-experiment1_gpr_files//1.1_Cy3_over_Cy5.gpr" >Error in readLines(con, n, ok) : invalid value for 'n' >In addition: Warning messages: >1: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >2: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >3: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >4: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >5: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >6: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >7: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >8: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) >9: input string 32 is invalid in this locale in: grep(pattern, x, >ignore.case, extended, value, fixed, useBytes) > > > >Does anybody now what's the problem here? > >Greetz, Tom