I am 1st time working on microarray data analysis...My chip is affy human gene 1 st. Using oligo package I have expression values at probeset level (RMA-probeset : around 2.6 lakhs of rows) and at transcipt level(RMA transcript : around 33 thosusands of rows).
My question if transcript level RMA gives gene level expression then what is RMA at probeset level ?
And how it differs with exon array 1 st?
Can I perform exon level analysis using Gene 1 st? It is mentioned on affymetrix site that gene1st is the subset of exon1st and it is very confusing for me.
Thank you in advance