[BioC] RMA vs VSN
Peter.Robinson at t-online.de
Mon Jun 21 12:39:01 CEST 2004
On Monday 21 June 2004 21:08, Roger Vallejo wrote:
> This must be of interest for those preprocessing data from affymetrix
> chips. We have compared RMA vs VSN performing an lme-ANOVA. If you are
> wondering what to use RMA or VSN? or what are the potential pitfalls or
> benefits from using either normalization or background data correction
> approach. Then, please read below and make your own conclusions.
> Thank you to the enlightening discussion followed up with colleagues at
> the Bioconductor group.
I'd like to throw another observation with request for comments into this
round. Our group has been using affymetrix murine chips with pooled samples
but no technical replicates as a way of identifying candidate genes for
further characterization by RT-PCR or in situ hybridization and other
techniques. We have used a simple fold-change threshold between samples taken
from different developmental stages or between wt and ko models to identify
Then, we are able to confirm about 80% of genes predicted following mas5
analysis (original or bioconductor is very similar).
However, rma analysis has produced lists of genes that are much shorter and in
general do not correspond well to the confirmed lists of genes produced by
mas5 (or to our biological prejudices as to what genes should be observed).
Have others notices similar discrepancies between mas5 and rma? Are there
perhaps other issues I have overlooked?
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