Thanks Kristina and Jose Manuel for your helpful replies.
What I do not fully understand about the filtering is the following: 
After Carboniferous, there are  ~3K Ans with non Ans values on the raw 
Value column, and that is out of ~2OK total genes, the range of those 
raw Values go from 2.95E-05 to 0.99. And there are other genes with 
similar Values that do not give NA on pad. And, of course, I do have 
genes that show 1 on the padj column.
It is a bit puzzling to me. I guess it depends on their level of expression?

Thanks!

Best,

David

Le 17/01/2014 17:57, Kristina M Fontanez a écrit :
>
> Hi David,
>
>> Hi Kristina,
>>
>> That was it indeed, thanks a lot. But then again, why do I not get 
>> them, the NAs I mean, when I do BH on the same data and the same 
>> contrast? That is:
>> results(dds,resultsNames(dds)[i],pAdjustMethod="BH")
>> Thanks again,
>> Best,
>> David
>
>
> One likely possibility:
> Independent Filtering is selecting the set of genes that results in 
> the most genes with adjusted p-values less than alpha 0.1 (by default 
> ON and ON in your function call above). Any genes with adjusted 
> p-values that do not pass filter are set to NA. If under the 
> Bonferonni correction there are genes with adjusted p-values above 0.1 
> then you will have NAs in your results. However, if under BH all of 
> your genes fall under the alpha 0.1 threshold, then you will have zero 
> NAs in your results.
>
> Kristina
> ------------------------------------------------------------------
> Kristina Fontanez, Postdoctoral Fellow
> fontanez@mit.edu <mailto:fontanez@mit.edu>
> Massachusetts Institute of Technology
> Department of Civil and Environmental Engineering
> 48-120E
> 15 Vassar Street
> Cambridge, MA 02139

-- 
David Rengel
Laboratoire des Interactions Plantes Micro-organismes (LIPM)
INRA/CNRS
24 Chemin de Borde Rouge
Auzeville
CS 52627
31326 Castanet Tolosan Cedex

E mail: david.rengel@toulouse.inra.fr
Tel 33 (0)5 61 28 55 91
Fax 33 (0)5 61 28 50 61

http://www.toulouse.inra.fr/lipm




	[[alternative HTML version deleted]]

