[BioC] normalise many cel files TCBB-2007-11-0161_noCEL.tar

[w langdon]

Dear Martin,
              Thank you for your quick and helpful reply.

On 1/1/13, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Bill --
>
> On 12/31/2012 11:20 AM, wlangdon [guest] wrote:
>>
>> Today I wrote to Rafael Irizarry about this and he suggested I post my
>> message here.
>>
>> Some time back I wrote some R code to normalise from
>> one to several tens of thousand Affymetrix cel files on a
>> (Linux) PC.
>>
>> The advantage is that it does not keep all cel files in memory
>> all the time and so the usual memory limits which restrict the
>> number of cel files do not apply.
>> http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp-code/R/TCBB-2007-11-0161_noCEL.tar
>>
>> The R-code also reports spatial defects:
>> A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips,
>> W. B. Langdon and G. J. G. Upton and R. da Silva Camargo and A. P.
>> Harrison, IEEE/ACM Transactions on Computational Biology and
>> Bioinformatics, 7(4) 647-653 oct-dec 2010. PubMed 21030732
>>
>> If we could incorporate this into your bioconductor affy package
>> that would be great.
>
> Thank you for the offer. Usually it is better to introduce code as an
> independent R package. There are instructions on how to do this available
> with R
>
>    RShowDoc("R-exts")
>
> and of course a  large number of miscellaneous web resources including our
> won
>
>    http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/
>
> Guidelines for the special expectations place on Bioconductor packages are
> at
>
>    http://bioconductor.org/developers/package-guidelines/
>
> Also if this sounds a little overwhelming then one possibility might be to
> suggest this as a 'mentored project'
>
>    http://bioconductor.org/developers/mentored-projects/
>
> for which a more experienced Bioconductor contributor would need to be
> identified as a mentor for you.

I'm afraid I am far from a bioconductor expert. So the 'mentored project' route
sounds idea. I have posted a reply to my orginal message asking
for a mentor.
Thanks again
Bill

> Martin
>
>>
>> Bill
>>
>>          Dr. W. B. Langdon,
>>          Department of Computer Science,
>>          University College London
>>          Gower Street, London WC1E 6BT, UK
>>          http://www.cs.ucl.ac.uk/staff/W.Langdon/
>>
>>
>>   -- output of sessionInfo():
>>
>> n/a
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>
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