[BioC] Normalization of exon arrays with expected global RNA degradation
ekspiulo at gmail.com
Fri Aug 5 21:24:43 CEST 2011
I'm considering alternate means to normalize an Affy Exon array
experiment of triplicate arrays over (non) induction of a condition and
(non) treatment in-vitro with an exoribonuclease. The same quantity of
RNA was selected for each array; however, we expect that there will be
some global or nearly global degradation of transcripts to a small
degree and many partially degraded transcripts among various of the 4
samples, and I'm looking to identify those transcripts which were
partially degraded in one sample compared to another.
I don't think RMA is appropriate for this dataset given that there
shouldn't be much real up or down regulation; however, there should be
some extremely common degradation effects in some of the samples.
What normalization approach might be useful here?
Department of Molecular Cellular Biology
The Ohio State University
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