I have been asked to do a gene level expression analysis of an experiment that used Affymetrix GeneChip Mouse Exon 1.0 ST Arrays:
When we had to analyse Affy exon arrays a decade ago, we found that the affy package was not able to handle them. We instead used to RMA normalize using the aroma.affymetrix package from CRAN, restricting to core probe-sets. We used to convert from exon to gene level expression summaries using the aroma.affymetrix function:
Ten years later, are there any recommended Bioconductor pipelines for normalizing and summarizing Affy exon arrays at the gene level? (Apart from the obvious advice to please do RNA-seq instead.)
I am aware of the xps and oligo packages but have not used either of them yet.