[BioC] Detection calls and LIMMA

[Wolfgang Huber]

Hi Avhena

it is not required, but properly applied filtering can increase 
detection power in your experiment while still controlling type-I error 
(false positives). The example you mention seems to be one that you want 
to keep though, since it is a good candidate for being up-regulated in 
the Treatment condition. One possibly reasonable criterion would be, 
e.g., to filter out all probesets that are called 'Absent' on all 
arrays. Some further discussion on the topic is also here:

[1] Bourgon, Gentleman and Huber. Independent filtering increases 
detection power for high-throughput experiments. PNAS, 107(21):9546-9551,

	Best wishes
	Wolfgang


Il Feb/28/11 6:51 AM, avehna ha scritto:
> Hi All,
>
> I have a basic question. Is it required to filter the microarray data based
> on the detection calls (A/M/P) before analyzing it with LIMMA?
>
> What if I have the following scenario (for example):
>
>                             Control Control Control         Treatment
> Treatment Treatment
> 1367813_at           A            A             P
> P                   P                 P
>
> Please note that this gene is just "present/detected"  once in the Control,
> but it is present in all the replicates of the treatment. In this case: what
> would be the right thing to do? To eliminate it from the analysis or keep it
> and consider it up or down depending on the signal of the treatment?
>
> Thank a lot!
> Avhena
>
> 	[[alternative HTML version deleted]]
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber