[BioC] Paired arrays and limma

[john seers (IFR)]

Hi James

A fortuitous coincidence you mention my name in a posting when I was
reading one of your threads the other day and this prompts me to ask you
directly.

The thread in question is:

 
https://stat.ethz.ch/pipermail/bioconductor/2007-November/020291.html


I followed the thread through and found it did not offer a solution and
you finish with:

"I'm not sure why you would want to do things pair-wise, but if you 
really want paired t-tests, then you will have to analyze the data in 
pairs rather than all at once."

I am using limma on a similar setup and I am not sure how to pair the
data. The setup is before and after two diets and a condition control
and disease. (There is a section in the limma manual on paired data and
a section on factorial designs but I am not sure how to marry them).

Can you explain what you mean by "analyzing the data in pairs rather
than all at once"? 

My solution so far is to preprocess the data and take the ratio of the
expression values of the paired arrays (so halving the number of
columns) and analyzing them in limma. That removes the pairing from the
limma analysis. Does that make sense to you?

Thank you in advance for any time you take.

Regards


John Seers 


 
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