[BioC] get full variance per gene from DESeq

[Wolfgang Huber]

Hi Graham

an alternative, and maybe easier and slightly more consistent approach 
might be to use the p-values (and the sign of the foldChange) to 
transform to z-scores, perhaps like this:

   with(BNevBTG,
      qnorm(pval/2) * sign(log2FoldChange)
   )


PS: "more consistent" because the residuals distribution (of the counts 
is skewed), while the p-values are uniform under the null.

  Best wishes
	Wolfgang

On Jul/30/10 11:47 AM, Graham Thomas wrote:
> Hi All,
>
> I am wondering whether there is an easy way of obtaining the full variance
> for a given gene and condition from my DESeq analysis?
>
> When I take a look at my results I end up with a table like so):
>
>  > head ( BNevBTG )
> id baseMean baseMeanA baseMeanB foldChange log2FoldChange
> 1 ENSMUSG00000001627 162.62034 119.50785 205.73284 1.7215006 0.78366671
> 2 ENSMUSG00000001630 45.51063 41.94099 49.08027 1.1702220 0.22678230
> 3 ENSMUSG00000001632 1626.19532 1328.32256 1924.06807 1.4484946 0.53455431
> 4 ENSMUSG00000001642 54.09075 54.53378 53.64772 0.9837521 -0.02363326
> 5 ENSMUSG00000001655 0.00000 0.00000 0.00000 NaN NaN
> 6 ENSMUSG00000001656 0.00000 0.00000 0.00000 NaN NaN
> pval padj resVarA resVarB
> 1 9.930922e-05 0.0005666467 0.4043083 2.7960349
> 2 4.628048e-01 0.6573258560 0.1815569 0.5295679
> 3 4.216269e-04 0.0021251136 0.3436054 0.3589968
> 4 9.559678e-01 1.0000000000 1.0424044 0.8391154
> 5 NA NA NA NA
> 6 NA NA NA NA
>
>
> I would like to transform my results into z-scores for GSEA purposes. As
> far as I understand in order to do this I require my baseMean value
> (which I have), my baseMeanA(and B) values, and the full variance (which
> I want).
>
> It may be noted that my practical statistics knowledge is HEAVILY
> limited so any helpp at all here is greatly appreiciated!
>
>
> Regards,
> Graham
>
>

-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber