[BioC] get full variance per gene from DESeq

[Graham Thomas]

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


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