[BioC] Limma 2.9.10: "Amean" missing

[Gordon Smyth]

Dear Julien,

The component 'Amean' in the output from lmFit() is supposed to hold 
the mean log-intensity for each probe, an indicator of the overall 
expression level of the corresponding transcript.

However, if the data values input to lmFit() are log-ratios rather 
than log-intensities, then there is no way to compute the mean 
log-intensities. If the first argument to lmFit() is a matrix, as it 
is in your simulation, then there is no way for the function to 
determine whether the input values are log-ratios or log-intensities. 
If they are log-ratios, then calculating Amean would be meaningless. 
Rather than risk computing a meaningless value, I stopped lmFit() 
from computing Amean in this situtation.

If the first argument to lmFit() is an MAList or exprSet or 
ExpressionSet then Amean is computed. It is actually not clear that 
this is right behaviour in the case of an ExpressionSet, but that's 
how it is for now.

Best wishes
Gordon

>Date: Thu, 15 Feb 2007 13:37:51 +0100
>From: Julien Gagneur <julien.gagneur at embl.de>
>Subject: [BioC] Limma 2.9.10: "Amean" missing
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <45D4541F.5020302 at embl.de>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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
>
>Room 62
>Meyerhofstrasse 1
>D-69117 Heidelberg
>Germany