[BioC] PreFiltering probe in microarray analysis

[Wolfgang Huber]

Hi Swapna

Il Jun/2/11 7:58 PM, Swapna Menon ha scritto:
> Hi Stephanie,
> There is another recent paper that you might consider which also
> cautions about filtering
> Van Iterson, M., Boer, J. M.,&  Menezes, R. X. (2010). Filtering, FDR
> and power. BMC Bioinformatics, 11(1), 450.
> They also recommend their own statistical test to see if one's filter
> biases FDR.
> currently I am trying variance filter and feature filter from
> genefilter package: try ?nsFilter for help on these functions.
> However, I dont use filtering routinely since choosing the right
> filter , parameters and testing the effects of any bias are things I
> have not worked out in addition to having read Bourgon et al and
> Iterson et al and others that discuss this issue.
> About your limma results, while conventional filtering may be expected
> to increase the number of significant genes, as the papers suggest
> likelihood of false positives also increases.

No. Properly applied filtering does not affect the false positive rates 
(FWER or FDR). That's the whole point of it. [1]

If one is willing to put up with higher rate or probability of false 
discoveries, then don't do filtering - just increase the p-value cutoff.

[1] Bourgon et al., PNAS 2010.

> In your current results,
> do you have high fold changes above 2 (log2>1)?  You may want to
> explore the biological relevance of those genes with high FC and
> significant unadjusted p value.
> Best,
> Swapna

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