[BioC] DESeq: help with analysis

Abhishek Pratap abhishek.vit at gmail.com
Tue Oct 15 19:50:27 CEST 2013

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


            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

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,
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