[BioC] Two populations on microarray

[Naomi Altman]

Dear Ben,
A typical MA plot has most of the points scattered around the line 
M=0.  Even if you have 2 populations of probes, the nondifferentially 
expressing genes should be in that central ellipse.  (The lower 
cluster does look somewhat like the typical MA plot for raw data.)  I 
suggest that you do separate MA plots for each population of probes, 
to see if one set of probes failed.  Or, as Gordon suggests, a 
population for which labelling failed.

--Naomi


At 05:48 PM 1/14/2012, Gordon K Smyth wrote:
>Dear Ben,
>
>Are you saying that you have deliberately designed two different 
>populations of probes onto your arrays?
>
>Your MA-plot suggests that there is substantial body of spots on the 
>array for which the green channel has failed, hence the 45-degree 
>line at the top of the plot.  These dots likely represent spots with 
>a normal red channel value but close to zero for green.  Normally 
>this would have a technical rather than biological cause.  An 
>imageplot may help you identify where the offending spots are on your array.
>
>On the other hand, if you have deliberately spotted your arrays with 
>two quite different populations of probes, then they probably need 
>to be analysed as separate arrays.
>
>Best wishes
>Gordon
>
>>Date: Thu, 12 Jan 2012 14:28:36 -0500
>>From: Ben Tupper <btupper at bigelow.org>
>>To: bioconductor at r-project.org
>>Subject: [BioC] Two populations on microarray
>>
>>Hello,
>>
>>By virtue of experiment design we have two populations to analyze 
>>on each of a suite of Genepix microarrays.  You can see an example 
>>in an MA plot here (generated using the excellent limma package) :
>>
>>         http://dl.dropbox.com/u/8433654/BE%20T46h%20slide%2052.png
>>
>>We have been following the steps in the limma user guide, and Ben 
>>Bolstad's helpful notes http://tinyurl.com/7346mh9 All of the 
>>examples we see appear to have just one population to contend with, 
>>which gives us an inkling that we are being naive about our 
>>analysis.  We suspect that we'll have to separate the two 
>>populations before normalization and analysis.  Are there any 
>>guides available for managing two populations like this?
>>
>>Thanks!
>>Ben
>>
>>
>>Ben Tupper
>>Bigelow Laboratory for Ocean Sciences
>>180 McKown Point Rd. P.O. Box 475
>>West Boothbay Harbor, Maine   04575-0475
>>http://www.bigelow.org
>
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