I'm using aroma.affymetrix R package to get exon level summaries. HuEx-1_0-st-v2 CDF file
I got exon level estimates from instructions at:
I cannot get transcript level information (FIRMA scores) working hence I would like to have gene level estimates.
For gene level summaries for which I got HuGene-1_0-st-v1 r4 CDF file.
I've V1 for HuGene and V2 for HuEx. Would that be an issue for downstream analysis?