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

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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880