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

[Martin Morgan]

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.

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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