I have a question. I am trying to normalize miRNA microarray data using VSN package. I am reading my CEL files with ReadAffy() function from affy. When I read the data :
RAW <- ReadAffy()
dim(exprs(RAW)) gives an output of 52900 rows which I cant explain. When I try to normalize this with affy package rma() function, a normal amount of rows : 7815 rows remain. However when I try to normalize this with justvsn() or vsn2() function what remains is again unexplainable 52900 rows. Do you guys know anything about VSN package not being used with ReadAffy() function or can you propose another way in which I can use VSN package? Thank you for your time.