Hi everyone,
I am analyzing a dataset where there is obvious 5' end RNA degradation. It was known before hybridizing the chip and we could not avoid this. In affy package, there is a function AffyRNAdeg()
which helps you assessing this trend.
But now that i'm sure that i have 5' end degradation, what can I do ? I was wondering if in the summarization process I could use only the 4 or 5 PM probes located at the 3' end, for example, but I did not find a function already dealing with that. Is anyone aware of such a way of summarizing affy data ? or do I have to write it myself ?
Thanks
Julien
thanks for this ! I'll do the usual way then.
Julien