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

[wlangdon [guest]]

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.

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/


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