[BioC] Filtering is not recommended with LIMMA?

[Wolfgang Huber]

Miriam:

To clarify: Bourgon et al. (2010) discourage the use of the limma t-statistic specifically with overall-variance filtering, since this invalidates type-I error control of the combined procedure. Either component by itself (limma t; or overall-variance filtering and normal t) is fine. Nobody yet seems to have worked out how to combine them (and it may not be worthwhile.)

I leave it to others to comment on I/NI filtering and limma.

Also, as Jelle Goeman notes, by combining the threshold on adjustedP and on FC (>1.4) you are being anti-conservative. This in combination with your filtering likely explains the effect you see.

Bottomline, by combing three criteria:
- limma-t
- I/NI
- FC cutoff
you are putting yourself into a difficult area of statistics, and unless you really know what you are doing, it might be best to deconvolute your criteria.

Best wishes
	Wolfgang

On 21 May 2013, at 03:06, "Garcia Orellana,Miriam" <mgarciao at ufl.edu> wrote:

> Dear Dr. Smyth.
> 
> Would you be that kind to help me on deciding whether yes or no to filter my microarray data set with a filtering method correcting for variance such as I/NI method from Talloen et al. (2007). Whereas many researchers say that filtering should increase the power of the test, then increasing the chance to get true deferentially expressed genes. However when I analyzed my data set. I found the next: (meaning lower number of DEG when filtering).
> 
> 
> 
> 
> Ortoghonal contrasts                # of genes
> (adjustedP >0.05 and   FC >1.4)
> w/o filtering   I/NI filtering
> FAT        195    118
> FA         329    151
> MR         169    103
> FAT by MR          854    321
> FA by MR          961     283
> 
> Also, I found that Bourgon et al. (2010) do not recommend to combine the use of  limma t-statistic with filtering. So please, I will appreciate your suggestion on whether filter or not filter my data set.
> 
> Thanks in advance.
> Miriam
> 
> 
> 
> ********************************
> Miriam Garcia, MS, PhD
> Department of Animal Sciences
> University of Florida
> 
> 
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