Thanks again Kristina. I'll have a close look at it.

PS: I do not know where on Earth the "Carboniferous" appeared from. What 
I meant was "Bonferroni". Funny.

Le 17/01/2014 21:22, Kristina M Fontanez a écrit :
> David-
>
> I’m sorry but I didn’t really understand your question. I don’t know 
> what you mean by Carboniferous, raw value (p-value?) or pad 
> (p-adjusted value?).
>
> However, this section (pg 8) of the vignette may help you determine 
> why you have NAs in the p-value column or the p-adjusted column in 
> your results() output (see pasted below). I would spend some time 
> reading the vignette and manual to help you answer these types of 
> questions. I’ve had to read them over several times to get the gist of 
> things and I’m still discovering new details!
>
> The results for particular genes can be set to NA, for either one of 
> the following reasons:
> 1. If within a row, all samples have zero counts, this is recorded in 
> mcols(dds)$allZero and log2fold change estimates, p-value and adjusted 
> p-value will all be set to NA.
>
> 2. If a row contains a sample with an extreme count then the p-value 
> and adjusted p-value are set to NA. These outlier counts are detected 
> by Cook’s distance. Customization of this outlier filteringis 
> described in Section 3.3, along with a method for replacing outlier 
> counts and refitting.
>
> 3. If a row is filtered by automatic independent filtering, then only 
> the adjusted p-value is set to NA. Description and customization of 
> independent filtering is decribed in Section 3.6.
>
>
> 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
>
>
>
> On Jan 17, 2014, at 3:11 PM, David Rengel 
> <david.rengel@toulouse.inra.fr <mailto:david.rengel@toulouse.inra.fr>> 
> wrote:
>
>> 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
>>
>>
>

-- 
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




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