[BioC] Limma 2.9.10: "Amean" missing

[Julien Gagneur]

Thank you Gordon to clarify this point.

In my context I am using it to extract mean log ratios, which I can get 
by other "means" :-)  anyway. I understand that it would be a safer way 
to proceed.

Best,

Julien.

Gordon Smyth wrote:
> 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
> 

-- 
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