Thanks Lorena and Steve.

Using the DeSeq2 I was able to get a list of genes after FDR adjustment. We
do some expected functional enrichment there which is great. I would be
curious to know the changes in DESeq2 but I guess the paper is not yet out.

Cheers!
-Abhi


On Tue, Oct 15, 2013 at 1:33 PM, Lorena Pantano <lorena.pantano@gmail.com>wrote:

> Hi,
>
> this could happen if your model doesn't explain all your design. There is
> good example in the tutorial about plotting pvalues to see if you get the
> expected distribution.
>
> Sometime I get the same, and in some cases, although FDR is not so low, if
> I do a heatmap of the top genes, I get my data clustered into the groups I
> have in my model (cases versus control for instance). So, sometimes there
> is signal even if FDR is higher than 0.1. But you need to be very careful
> and really look your data using other visual representation as others have
> suggested.
>
> cheers
>
>
>
>
> Lo
>
>
> On Tue, Oct 15, 2013 at 7:50 PM, Abhishek Pratap <abhishek.vit@gmail.com>wrote:
>
>> Hi Everyone
>>
>> Given the study design( see below) I am somewhat surprised NOT to see any
>> genes being differentially expressed with p.adj < .05 or .10. I would like
>> the help from folks on this mailing list to introspect the analysis and
>> figure out if we overlooked something or data
>>
>>
>> Study Design:
>> 4 cases v/s 4 control ( all replicates are biological)
>> One sample in the case had very low read counts but I thought that should
>> not make a lot of difference in case of DESeq. I did however try to re-run
>> the analysis taking that out but no change as far as the #diff exp genes.
>>
>> Analysis done with : DESeq_1.12.0
>>
>> > sizeFactors(cds)TRA00010811 TRA00010812 TRA00010816 TRA00010813
>> TRA00010814 TRA00010817 TRA00010818
>>
>>   0.9834455   1.3122005   0.7464998   1.3739400   1.6820479
>> 0.5693563   0.7763204
>>
>>
>>
>> metadata
>>
>>
>>             condition    libType
>> TRA00010811   ablated paired-end
>> TRA00010812   ablated paired-end
>> TRA00010816   control paired-end
>> TRA00010813   ablated paired-end
>> TRA00010814   ablated paired-end
>> TRA00010817   control paired-end
>> TRA00010818   control paired-end
>>
>>
>>
>> Attached:
>> dispersion plot and MA plot
>>
>> Please let me know if you need anything more from my end to help me dig a
>> bit deeper and understand what might be going on here.
>>
>> Thanks a lot,
>> -Abhi
>>
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>>
>
>

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