[BioC] edgeR and sagenhaft

[Mark Robinson]

What are the library sizes?


On 19/02/2009, at 3:06 PM, Naomi Altman wrote:

> Here is some of the discrepant output.   A1, A2, B1, B2 are the 4
> samples with tag counts.
>
> My commands were
> y=cbind(A1,B1,A2,B2)
> d<- DGEList(data = y, group = c(1,2,1,2), lib.size = apply(y,2,sum))
> alpha <- alpha.approxeb(d)
> ms <- deDGE(d, alpha = alpha$alpha)
>
> Here are the first 5 cases where both samples had Fisher's exact test
> p-values <.001 and the edgeR exact statistic >.05.  These
> are raw p-values.
>
>
>          A1            B1          A2         B2
> Sagenhaft p-value A1 vs B1       Sagenhaft p-value A1 vs B1        ms 
> $exact
>          46           5           39          12
>  7.546362e-11                          3.605042e-06
>       0.76524756
>          33           4           45          13
>  1.128468e-07                          3.791248e-07
>       0.97325389
>           0          55           13          49
>  1.070343e-15                          1.668152e-04
>       0.08834922
>        69         179           92         526
> 2.088333e-09                          3.816029e-55
>     0.56544378
>     109          36          122          63
> 3.988028e-12                          4.556175e-09
>     0.86574462
>
>
>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348  
> (Statistics)
> University Park, PA 16802-2111
>
> 	[[alternative HTML version deleted]]
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852