[BioC] Filtering affymetrix data

[Teresa Casals]

Hello

I have been involved recently in analyzing some
microarray experiments performed with affymetrix
chips.

This task had been previously done by another analyst
who left me some scripts, but no explanations.

The procedure she used to follow was first to
normalize the arrays, say using rma and then, before
doing any tests she used to apply two filters

- She kept only those genes whose signal was greater
than a threshold on all arrays (she used "log(100)" as
this threshold)
- Assuming for simplicity that there were only two
groups she applied a second filter keeping only those
genes where the base-2 logarithm of the difference
between the mean of the two groups was greater than
1.5

I think I understand the rationale under this
procedure, but also I find it somewhat arbitrary.

Could someone please orient me about if this a
usual/right way to proceed, or address to some
references or examples which help to diminish the
feeling of arbitrarity?

Thanks for your help

========================
Teresa Casals