Entering edit mode
8.6 years ago
alptaciroglu
•
0
Hello,
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.
One is most likely summarising your data per gene (i.e. taking expression values from exons and producing a single expression value per gene), whilst the other (VSN) is just analysing all data-points independently.
Which array are you using?; which species?
Check all command-line parameters to each program and ensure that you know what each is doing and which are the default values.