FIRMAGene is an R software package for using Affymetrix Gene 1.0ST arrays to detect differential splicing events.
See the following manuscript:
Robinson MD and Speed TP
Differential splicing using whole-transcript microarrays
BMC Bioinformatics 2009, 10:156 [PubMed Abstract]
[06-June-2009] The package is now hosted by R-forge and is available from here.
[12-June-2009] Due to some changes in underlying packages, the sup3.R script has been updated.
[28-June-2009] For those of you using MoGene, you will notice that the script (sup3.R) does not run smoothly, since the probetab file you can get from Affymetrix contains probe coordinate mappings from mm8, whereas you can only get mm9 mappings from biomaRt. I have now created a CDF file and new probe mapping TXT file so that users can use biomaRt/GenomeGraphs to display the FIRMAGene results. To do that, download the (gzipped) CDF from here, the new (gzipped) probetab txt file from here and run commands in R similar to those in this file. Thanks to Scott Davis for portions of the script. For those interested in how this was done, see the R commands in this file.
[28-June-2009] I've now committed changes to FIRMAGene version 0.9.5 so that users can track which subset of probes contribute to the extreme MUF score. See the 'plm' and 'cls' arguments fo the topSplices() function near the end of this R commands file. The results for the Affymetrix MoGene tissue panel dataset can be found in PDF and CSV format, from running that script.
[04-Feb-2010] Made a modification to the sup3.R script, now available as sup3_04feb2010.R, to make sure we use the Ensembl annotation that corresponds to the hg18 (Mar 2006) build.
NB: This package is an ALPHA release and it relies heavily on the R aroma.affymetrix package. When time permits, it is my plan to migrate the FIRMAGene code to aroma.affymetrix so that it can share the same memory efficiency and user support. In the meantime, please give feedback directly to me, at MROBINSON [at] WEHI [-dot-] EDU [-another dot-] AU.