Hi,
If I understood it right, the independent filtering uses parameters to optimise the results after the correction, and hence it could be affected by the adjustment method chosen. But let the authors confirm it.
Best
Jose

On 17 Jan 2014, at 17:44, David Rengel <david.rengel@toulouse.inra.fr<mailto:david.rengel@toulouse.inra.fr>> wrote:

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

Le 17/01/2014 17:28, Kristina M Fontanez a écrit :
Hi David-

If you look at the description of results() in the manual then you
will see that by default independentFiltering is turned ON. I think
this is your likely culprit given that your results function call
doesn’t explicitly turn OFF independent filtering.

pg.27: "By default, independent filtering is performed to select a set
of genes which will result in the most genes with adjusted p-values
less than a threshold, alpha. The adjusted p-values for the genes
which do not pass the filter threshold are set to NA. “

Best,
Kristina
------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto: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



On Jan 17, 2014, at 11:20 AM, David Rengel
<david.rengel@toulouse.inra.fr<mailto:david.rengel@toulouse.inra.fr> <mailto:david.rengel@toulouse.inra.fr>>
wrote:

Hi,

I would be grateful if you could help me out on this one. Why do I get
NA for certain genes on the padj column when I do this:


results(dds,resultsNames(dds)[i],pAdjustMethod="bonferroni")


I do not get them when I do BH


Thanks for your help


Best,

--
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<mailto:david.rengel@toulouse.inra.fr>
<mailto: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


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--
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<mailto: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




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