[BioC] fRMA for Gene ST arrays

[Matthew McCall]

Kamila,

You can preprocess Gene ST arrays using the latest version of frma --
just load the data using the oligo package. And you can obtain GNUSE
values using the GNUSE function on the preprocessed data object.

A barcode implementation for the Gene ST arrays is not currently
available, but it is in the works -- hopefully it will be ready before
the fall BioC release.

Best,
Matt


On Wed, Apr 3, 2013 at 8:41 AM, Naxerova, Kamila
<naxerova at fas.harvard.edu> wrote:
> Dear list,
>
> to preprocess Affymetrix whole transcript arrays, use of oligo and xps is recommended over the affy package. I am interested in using the GNUSE algorithm to assign quality scores to some arrays, and would also like to try out the barcode function in the frma package. I am now wondering... is frma compatible with whole transcript arrays?
>
> Thanks a lot.
> Kamila
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Matthew N McCall, PhD
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