[BioC] readGPR (arrayQuality)

[Gordon Smyth]

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