[BioC] readGPR (arrayQuality)

[Paquet, Agnes]

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

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