[BioC] Limma analysis of focused arrays vs. whole genome arrays

[A.J. Rossini]

I would've rephrased the problem differently:

Given that you can't depend on the "typical" assumption of
"zero-expression", what features should you design in for
comparability?

The idea of housekeeping genes seems sensible in theory -- in
practice, I'm not sure how to protect from inadvertent "discovery".

best,
-tony


On 6/7/05, Mike Schaffer <mschaff at bu.edu> wrote:
> Hi,
> 
> The lab I work with has used "whole genome" human arrays (~18,000
> genes) for a couple years and I have helped with the analysis using
> Limma.  Now, due to costs, they are now considering switching from
> whole genome arrays to focused arrays with ~400 genes of interest
> (selected from the whole-genome array results).
> 
> The obvious analysis problems with a focused array where most genes are
> changing are:
> 
> 1. LOESS normalization assumes most genes are not changing.  If most of
> the genes are expected to change, there is no basis to recenter the
> data around zero.  The response from the lab was that they would be
> willing to include 100-150 genes that are not expected to change.
> 
> 2. The B-statistic in Limma requires a parameter indicating a certain
> fraction of genes are changing.  The corresponding moderated
> t-statistic uses the data from all genes to moderate the standard error
> in the t calculation.  Both of these could change dramatically if most
> of the genes on the array are changing.
> 
> 
> My questions are:
> 
> 1. Are my concerns valid and are there ways around around them?  Are
> there other analysis pitfalls with this scenario?
> 
> 2. Can Limma handle situations where most of an array is expected to
> change?  What modifications, if any, need to be made to the Limma
> analysis to account for this?
> 
> 3. Alternatively, is there a more appropriate statistical package to
> use in this case?
> 
> 
> Thanks.
> 
> --
> Mike
> 
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-- 
best,
-tony

"Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes" (AJR, 4Jan05).

A.J. Rossini
blindglobe at gmail.com