[BioC] vsn and oligo (or xps?) packages for GeneST expression arrays

Tim Rayner tfrayner at gmail.com
Mon Jan 4 15:06:33 CET 2010


I'm curious to know whether there are any plans to support the use of
the VSN algorithm (i.e. the vsn package) with the classes defined by
the oligo package. The reason I ask is that it seems as though the
latter package is now touted as one of the supported methods of
handling Affymetrix GeneST expression arrays (e.g. HuGene, MoGene),
but as far as I can see the only expression
normalisation/summarisation method currently supported for objects of
the oligo GeneFeatureSet class seems to be RMA. I'm not even sure if
GCRMA is supported for GeneFeatureSet objects? I guess the same
questions also apply to the xps package, although I suspect that VSN
support would turn out to be more work to implement there given the
rather different underlying object structures used by xps. Do please
correct me if I'm wrong about any of this, but until now I've been
forced to shoehorn our data into the old AffyBatch workflow using
custom CDFs and I'd like to know if there's a better (i.e. supported)
workflow I could be using.

Best regards,

Tim Rayner

# Current setup for reference:
> sessionInfo()
R version 2.10.0 Patched (2009-11-03 r50305)

[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] oligo_1.10.0         preprocessCore_1.8.0 oligoClasses_1.8.0
[4] gcrma_2.18.0         vsn_3.14.0           affy_1.24.2
[7] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affxparser_1.18.0 affyio_1.14.0     Biostrings_2.14.8 DBI_0.2-4
[5] grid_2.10.0       IRanges_1.4.9     lattice_0.17-26   limma_3.2.1
[9] splines_2.10.0

Smith Lab, CIMR
University of Cambridge

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