[BioC] Limma 2.9.10: "Amean" missing

[J.delasHeras at ed.ac.uk]

Q
Nope, I just tried it (limma 2.9.10 under R2.4.1) and it's there.

What has changed is topTable, from limma 2.9.3:

   "Changes to column headings from topTable: M is now logFC,
   A is now AveExpr"

that threw me out at first as I didn't read the changeLog :-)

Jose



uoting Julien Gagneur <julien.gagneur at embl.de>:

> Hi,
>
> I miss the Amean field in the output of eBayes() in limma 2.9.10 .
>
> It is there in limma 2.8.1
>
> sample code:
>
> #  Simulate gene expression data,
> #  6 microarrays and 100 genes with one gene differentially expressed
> set.seed(2004); invisible(runif(100))
> M <- matrix(rnorm(100*6,sd=0.3),100,6)
> M[1,] <- M[1,] + 1
> fit <- lmFit(M)
>
> #  Ordinary t-statistic
> par(mfrow=c(1,2))
> ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma
> qqt(ordinary.t,df=fit$df.residual,main="Ordinary t")
> abline(0,1)
>
> #  Moderated t-statistic
> eb <- eBayes(fit)
>
>
> # this returns FALSE with limma 2.9.10, TRUE with limma 2.8.1
> "Amean" %in% names(eb)
>
>
>
> I run R 2.4.1. Do you experience the same?
>
> Thanks,
> Julien.
>
> --
> Julien Gagneur
> EMBL/HTFG Center
> Tel: +49-(0)6221-387-8433
> Fax: +49-(0)6221-387-8166
> Email: julien.gagneur at embl.de
>
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>
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>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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