[BioC] Display of histogram of RMA-processed data

Lawrence-Paul Petalidis lpp22 at cam.ac.uk
Thu May 13 17:46:01 CEST 2004

Hello all
I have seen such post RMA hist plots in my data too (human tumours on
U133A chips). I did not see a nice smooth curve but curves that looked
very similar to yours (two peaks etc). I think there is nothing wrong
with the data, it probably has to do with the way you plot it. Indeed,
if you use plot(density(exprs(rma), bw="nrd0", adjust=1)) instead and
play around with the adjust value you will see that you can actually
smoothen the way the data looks in the plots. This actually alters the
width used for plotting I believe (?). I would be interested to hear
what everybody thinks about this. 

Yours kindly, Lawrence

Lawrence-Paul Petalidis
Ph.D Candidate
Department of Pathology
Division of Molecular Histopathology
University of Cambridge

		-----Original Message-----
		From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Richard
		Sent: 13 May 2004 16:21
		To: James MacDonald
		Cc: bioconductor at stat.math.ethz.ch
		Subject: Re: [BioC] Display of histogram of
RMA-processed data

		On May 13, 2004, at 10:35 AM, James MacDonald wrote:

			Try plotDensity(exprs(howard1.norm))

		Jim (and everybody),
		Jim, Thanks for your advice.
		I am somewhat puzzled at the outcome. Here is is the
hist plot of the unnormalized data:
		 << File: howard1.raw.hist.pdf >>  << File:
howard.norm2.hist.pdf >>  << File: howard1.norm.plotdensity.pdf >>  <<
File: howard1,raw.plotDensity.pdf >> 

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