Hi list,

I am working with single color data from Agilent platform. After the limma
analysis the adjusted p values were higher than 5% of FDR. At this instance
I am thinking of filtering the genes using genefilter. As my data set
contains only raw intensities of normal and test before the normalization,
where I am uisng 'normalizeBetweenArrays' command after log transforming the
data.
In this scenario I am quite confused whether I should use the filter
functions prior to normalization of after the normalization but efore
fitting the linear model?
As my data is not an expressionSet I cannot use the nonfilter commands, in
this case any suggestions of using other filtering methods?

Appreciate the suggestions

-- 

Regards,
Abhilash

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