[BioC] PreFiltering probe in microarray analysis
whuber at embl.de
Sat Jun 11 23:36:35 CEST 2011
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. 
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.
 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.
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