[BioC] Help in reading .gpr file in Linux by using the read.maimages

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Hi Alex,

Alex Tsoi wrote:
> Dear all,
> 
> I am struggling to input .gpr by using the " read.maimages " command in the
> linux machine
> 
> The try2.gpr file has the column names:
> 
> Block    Column    Row    Name    ID    X    Y    Dia.    F635 Median
> F635 Mean    F635 SD    B635 Median    B635 Mean    B635 SD    % >
> B635+1SD    % > B635+2SD    F635 % Sat.    F532 Median    F532 Mean    F532
> SD    B532 Median    B532 Mean    B532 SD    % > B532+1SD    % > B532+2SD
> F532 % Sat.    Ratio of Medians (635/532)    Ratio of Means (635/532)
> Median of Ratios (635/532)    Mean of Ratios (635/532)    Ratios SD
> (635/532)    Rgn Ratio (635/532)    Rgn R² (635/532)    F Pixels    B
                                           ^
                                     the culprit (I guess)

> Pixels    Sum of Medians    Sum of Means    Log Ratio (635/532)    F635
> Median - B635    F532 Median - B532    F635 Mean - B635    F532 Mean -
> B532    F635 Total Intensity    F532 Total Intensity    SNR 635    SNR
> 532    Flags    Normalize
> 
> 
> and when I read it by using:
> 
>> mraw <- read.maimages("try2.gpr", columns=list(R = "F635 Median", G="F532
> Median", Rb="B635 Median", Gb="B532 Median"),
> annotation=c("Block","Row","Column","ID","Name"))
> 
> I get the error messages:
> 
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>         Specified column headings not found in file
> In addition: Warning message:
> input string 1 is invalid in this locale in: grep(pattern, x, ignore.case,
> extended,value, fixed, useBytes)
> 
> 
> So, I try to use the same command in my PC, and it can successfully read the
> try2.gpr file. Both my PC and the linux machine are using the same R and
> Bioconductor version.

Which are? Please provide the output of sessionInfo() when you report a problem.
sessionInfo() will probably indicate a different LC_CTYPE (i.e. a different charset)
on Linux and your "PC" (I guess you mean Windows here).
Also sessionInfo() would tell us which version of limma you are using. Are you sure
it's recent enough? Maybe this problem has been fixed in more recent versions.

You're probably using a multibyte charset on your Linux box (which distro are you
using?), like e.g. UTF8, but the file that you are trying to read contains char codes that
are invalid in your charset. You can try to replace field "Rgn R² (635/532)" by e.g.
"Rgn R^2 (635/532)" in the file or update limma and see if this solves the problem.

Cheers,
H.


> 
> Does anyone know what's the problem here ? I greatly appreciate for any
> suggestion.
> 
> 
> Thanks,
> Alex -
> 
> Medical University of South Carolina
> 
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> 
> 
> 
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