[BioC] how to revert to an older limma version?

[Martin Morgan]

Hi Maya -- Here are my suggestions. Most important, cut and paste
command and results from your R session, so that we can see what is
going on

1. Please, please include the output of sessionInfo(). You can cut and
   paste this from your R session into the email. Do this after you
   have reproduced the error. 

2. Report the exact command that causes the error, and error message.
   Do this by copying and pasting the relevant portions of your R
   session. For instance, we do not yet know whether you provide your
   own column names, or what type of files you are trying to read.

3. After the error occurs, run the command traceback() and include the
   results. This shows where the error likely occured

4. evaluate the command

> oldOpt = options(warn=2)

   (this will cause the warning to become an error), rerun the command
   and report the results of traceback(). This will indicate where the
   suspicious warning about 'grep' occurs.

5. Does the error occur when only some files are used for input, or
   does it occur with any file? If it is with only some files, then
   can you verify that the column names are present in those files?
   Can you determine the character encoding of those file, for
   instance by opening them in a browser such as firefox and looking
   at View --> Character encoding.

Martin   

"Maya Bercovich" <MayaB at tauex.tau.ac.il> writes:

> -----Original Message-----
> From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
> Sent: 09 July, 2007 11:18 PM
> To: Maya Bercovich
> Cc: Marcus Davy; Kasper Daniel Hansen; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] how to revert to an older limma version?
>
> "Maya Bercovich" <MayaB at tauex.tau.ac.il> writes:
>
>> See bellow and thank you so much.
>
> In general, I would recommend using the most recent version of limma.
> It would be helpful to include the output of sessionInfo() after the
> error occurs.  The error message does suggest a locale or encoding
> mismatch.  Can you try setting your locale to "C":
>
>    Sys.setlocale(locale="C")
>
> I tried it, and I still get the same error. Any more suggestions?
>
> Appreciate your assistance,
>
> Maya
>
>
>
> + seth
>
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
> Center
> http://bioconductor.org
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org