[BioC] density plot of pm values

[Naomi Altman]

I am used to seeing 2 modes, although the second mode has been 
further to the left on the (older, whole genome) chips I have seen.

--Naomi

At 02:05 PM 11/28/2011, James W. MacDonald wrote:
>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.
>
>Best,
>
>Jim
>
>
>>
>>I would appreciate any ideas as to the rasons behind this behavior.
>>
>>Thanks
>>A.
>>
>>
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>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Douglas Lab
>University of Michigan
>Department of Human Genetics
>5912 Buhl
>1241 E. Catherine St.
>Ann Arbor MI 48109-5618
>734-615-7826
>
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