[BioC] Limma B statistic

Darlene Goldstein darlene.goldstein at epfl.ch
Tue Dec 21 16:30:06 CET 2010

Sabrina AT Case <hxs61 at ...> writes:

> Hello, all
> I am using Limma for my array analysis. Based on the user's guide, I
> canconvert B value to probability.
> however, in my results, I have adj.P.Val of 0.007 with B negative. If
> I use the conversion, the probability will be 0.25. But when you look
> at the p value, it passed the significant 0.05 level. How can I
> explain that? Did I misunderstand some points? Thanks
> Sabrina
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hi, It looks to me like you are confusing the p (or adj p) value with the B-stat
probability. The (adj) p-value reported in the topTable function is associated
with the mod-t statistic and is not related to the B-stat probability. The
B-stat probability is obtained by converting the log odds ratio to obtain the
probability p.

Does this clear up your question?

Best regards,


Darlene Goldstein
École Polytechnique Fédérale de Lausanne (EPFL)
Institut de mathématiques
Bâtiment MA, Station 8        Tel: +41 21 693 0528
CH-1015 Lausanne              Fax: +41 21 693 4303

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