[BioC] Exclude probes that show sd above 0.1between replicatevalues

[J.Oosting at lumc.nl]

Hi Jose,

IMHO you should use the variability of replicate spots whenever
possible. Limma can handle this nicely and for the analysis of
differential expression I always leave in the replicate spots, and I let
limma handle them.

For presentation purposes (i.e. heatmaps) it is usually handy to have
averaged values per gene, and I think that removing genes that cannot be
measured reliably is a way of improving the visualizations.

Any data-manipulation is context dependent, and especially the effects
of removing data points should be considered case by case. If you're
interested in on/off phenomena you should not remove 'empty' spots.

Regards,

Jan

> 
> If you look at the variation on M values alone (it's a 
> MAList), and throw away those with high variation... that 
> sounds like a reasonable thing to do, except that when you 
> have spots with no signal in only one of the channels, the 
> variation is probably quite high too, and you'd remove them. 
> However, they are probably quite an interesting class of 
> spots to keep (genes that become silenced, or activated, 
> after treatment, not merely down/upregulated).
> 
> I'm mostly studying experiments when I am interested mostly 
> in these cases of activation/silencing, and not so much in 
> up/downregulation alone. I wonder how people account for 
> these situations...
> 
> Jose
>