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

Benilton Carvalho bcarvalh at jhsph.edu
Mon Jan 4 16:32:04 CET 2010

Hi Tim,

yes, vsn support is planned. The affy and oligo packages share methods with the same name which come to be a problem when adding support for vsn. We already have agreed on a solution and it's just a matter of implementing these changes, which will greatly simplify this task.

As soon as something is available (on the devel branch), I'll get back to the list.



On Jan 4, 2010, at 2:06 PM, Tim Rayner wrote:

> Hi,
> 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)
> x86_64-apple-darwin9.8.0
> locale:
> [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
> --
> Bioinformatician
> Smith Lab, CIMR
> University of Cambridge
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