[BioC] Limma package: problem with p-value and t
James W. MacDonald
jmacdon at med.umich.edu
Thu Sep 17 22:50:38 CEST 2009
Julie Zhu wrote:
> Dear Gordon,
>
> I noticed that there is inconsistency between the t and p.value on the
> topTable output using Limma package to analyze a dye swap two channel array
> experiment.
> logFC AveExpr t P.Value adj.P.Val B
> 1401 3.216254 11.74137 22.49546 1.041470e-05 0.07874703 3.435097
> 1537 3.344735 11.88007 18.07448 2.702061e-05 0.07874703 2.951114
>
> The two-tailed p-value for t=22.49546 with df=1 would be 0.028
> 2*pt(-abs(22.49546),df=1), but the P.Value in the above output is 1.04e-05.
> Did I miss something? Could you please explain the inconsistency? Thanks!
The degrees of freedom will be somewhere around 3, but a bit larger
because of the ebayes fit. You can get the actual value from your
MArrayLM object, so what you really want is
2*pt(-abs(22.49546), fit$df.prior + fit$df.residual[1])
assuming you did something like
fit <- lmFit(<stuff>)
fit <- eBayes(fit)
Best,
Jim
>
> Here is the design matrix and relevant code snippets.
>
> Dye mutant
> 1 -1
> 1 -1
> 1 1
> 1 1
>
> design = cbind(Dye=1, mutant = c(-1,-1,1,1))
> fit = lmFit(MA, design)
> ### MA is a MAlist object
> fit3 = eBayes(fit)
> topTable(fit3, number=2, coef="mutant", adjust="fdr")
>
> Here is my R session information.
>
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] limma_2.18.0
>
> Thank you very much for your help!
>
> Best regards,
>
> Julie
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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734-615-7826
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