[BioC] Error message from R2.2.0 on Linux

[Kasper Daniel Hansen]

On Dec 6, 2005, at 10:04 AM, Hua Weng wrote:

> Hi, All:
>
> Is there anybody have problem running limma 2.2.4 from R 2.2.0 on  
> Linux? I can run the same code for Limma 2.2.4 from R2.2.0 on  
> windows without any problem. The following is information for R   
> and limma on linux:
>
>> version
>          _
> platform i686-pc-linux-gnu
> arch     i686
> os       linux-gnu
> system   i686, linux-gnu
> status
> major    2
> minor    2.0
> year     2005
> month    10
> day      06
> svn rev  35749
> language R
>
> limma        "limma"        "/usr/local/R/lib/R/library" "2.4.4"
>
> And the following is the error message from the command:
>> library(limma)
>> files <- dir(pattern=".gpr")
>> RG <- read.maimages(files, columns=list(R="F532 Mean", G="F635  
>> Mean", Rb="B532 Median", Gb="B635 Median"), wt.fun=wtflags(0.1))
> Error in switch(source2, quantarray = { : Cannot find column  
> heading in image output file
> In addition: Warning message:
> input string 32 is invalid in this locale in: grep(pattern, x,  
> ignore.case, extended, value, fixed, useBytes)
>
> I highly appreciate any comments and suggestions for this error.

Guess: you are reading in a textfile which contains non-standard  
characters, eg. special letters etc. You are currently operating in a  
local which does not support this particular character, so either  
change the locale or change the file. I see you are based in the US,  
so I am a bit surprised that you are having problems with this.

Do a
# env
from the shell to get a list of variables, I think the locale one is  
called
  LANG
(if you have variables such as LC_**** they override the LANG settings).

However, I would change the file. Further debugging requires a look  
at the header of the file.

Kasper

> Hua Weng
> Microarray Core Facility
> 348E Noble Research Center
> Department of Biochemistry and Molecular Biology
> Oklahoma State University
> Stillwater,  OK  74078
> Phone:  405-744-6199
> Fax:  405-744-7799
>
>
>
>
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>
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