is it possible to use RMA to get exon-level summaries for the HTA 2.0 platform in Bioconductor?
I would like to run diffSplice() from limma to detect genes that have evidence for differential splicing between two conditions and I need an expression matrix with counts at the exon level for that.
I have already used RMA on the probeset/transcript cluster level using the Affymetrix hta20 annotation data (hta20transcriptcluster.db) but I couldn’t find a Bioconductor annotation data package for the exon level for HTA 2.0.
I have also used a custom CDF for HTA 2.0 from Brainarray (which maps transcript cluster IDs to exon IDs) for the FIRMA analysis (method for the detection of alternative splicing from exon array data) as implemented in the Aroma Affymetrix framework.
However, I would like to compare my results gained by the FIRMA analysis with those of an alternative method, preferably with a solution based on Bioconductor packages.
I would be very thankful for any help!