
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
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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

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