I'm working with exon level microarray analysis. I've two annotation files - probeset and transcripts. I normalize data on two targets - gene and probesets to get estimates at gene level and exon level respectively.
After filtering genes that aren't in probeset annotation and probesets for which genes aren't available I end up with 17K genes and 580K exon probesets.
Is there a way I can filter these 580K probesets? How?
I cannot find any function in oligo to calculate dabg.
Second, can I only work with probesets that are main? filtering probes in affymetrix data
I have 228349 probesets that are main.
I maybe wrong in using correct terminology (exon, exon probsets), please correct and pardon me.