[BioC] edgeR and sagenhaft

[Naomi Altman]

A1                 B1               A2             B2
1376421      1577198      1948700      2448499



At 11:48 PM 2/18/2009, Mark Robinson wrote:

>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
>------------------------------
>
>
>
>

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