[BioC] Nobody wants to comment on this? post justRMA hist plots

Rafael A. Irizarry ririzarr at jhsph.edu
Mon Dec 15 21:44:51 MET 2003

i dont see any problems with those plots. if you are worried about the 
unsmoothness around the mode its probably due the smoothing criteria 
used in the density estimator not being large enough for your data. 
look at the code for plotDensity or simply use

for(i in 1:ncol(exprs(rma_eset)))

to see that there is really no problem. make nclass big enough and the 
histograms start getting rough. thats true for any continuos data.

On Mon, 15 Dec 2003, Lawrence 
Paul Petalidis wrote:

> 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
> ______________________________
> Lawrence Paul Petalidis
> Ph.D. Candidate
> University of Cambridge
> Department of Pathology
> ______________________________

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