[BioC] density plot of pm values

James W. MacDonald jmacdon at med.umich.edu
Mon Nov 28 20:05:10 CET 2011

Hi Assa,

On 11/28/2011 7:48 AM, Assa Yeroslaviz wrote:
> Hello BioC Users,
> I have a problem interpreting my data.
> I am analyzing my microarray data and did a density plot of my pm values
> for the six arrays.
> I am getting a strange behavior of these arrays. Instead of getting one
> peak for the data as it is usually is ( at least as fat as I know it), I am
> getting two peaks (see the image attached).
> The good news is that they all behave similarly, so it might be normal, but
> I just don't get it.

It depends on the chip, IME. The Gene ST and Exon chips tend to have 
this distribution, whereas the older 3'-biased chips seemed to me to be 
more unimodal.



> I would appreciate any ideas as to the rasons behind this behavior.
> Thanks
> A.
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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