[BioC] Two populations on microarray

[Gordon K Smyth]

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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