[BioC] AffylmGUI Comparisons and Filtering

[Quentin Anstee]

Hi,

I am new to microarray analysis with R and so have found the AffylmGUI
package a great help. I was wondering whether there is any way to filter the
gene lists (as I guess you can with filterfun to weed out those genes where
expression is too low on some arrays, etc and so reduce the number of genes
that as being simultaneously tested) and then still benefit from the ease of
use of the AffylmGUI package?

Also, I would like to do a three way comparison (A vs B, A vs C and B vs C).
When I select 'Compute Contrasts' it provides n-1 possible contrasts. Is it
reasonable to do this by setting up three separate contrast
parameterizations (one for each contrast pair above)?

Very many thanks for any advice.

Best wishes,

Quentin


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