[BioC] post justRMA hist plots

Lawrence Paul Petalidis lpp22 at cam.ac.uk
Fri Dec 12 12:35:21 MET 2003

Dear All
Any help with this would be appreciated. I am normalizing a number of U13A
affy chips with justRMA and upon comparison of the pre- and
postnormalization histogram curves, I see what seem to be some anomalies in
the post-normalization ones. The post-normalization curves that I have seen
from other people most often look much smoother than what I get. I attach
two graphs for you to inspect if you wish. 4 chips were used only, all of
excellent quality check indices (intensity, gene representation, noise etc).

> library(affy)
> eset <- ReadAffy() # read in 4 affy U133a chips
> hist(eset) # see pre-RMA plot attached
> rma_eset <- justRMA()
> plotDensity(exprs(rma_eset),col=”red”,xlab=”log intensity”) # see post-RMA
plot attached

I see the same phenomenon when I work with all 69 of my chips. Ive also
tried justRMA-ing the entire set in small 5-chip batches to see if one or
more chips in particular may be responsible, but it seems to be a rather
widespread issue.

Thank you for you kind attention.

Lawrence Paul Petalidis
Ph.D. Candidate

University of Cambridge
Department of Pathology

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