[BioC] limma

[Wolfgang Huber]

Hi Gordon

> .... "limma ensures that all probes are
> assigned at least a minimum non-zero expression level on all arrays, in
> order to minimize the variability of log-intensities for lowly expressed
> probes. Probes that are expressed in one condition but not other will be
> assigned a large fold change for which the denominator is the minimum
> expression level. This approach has the advantage that genes can be
> ranked by fold change in a meaningful way, because genes with larger
> expression expression changes will always be assigned a larger fold
> change."

I am not sure I follow:

(i)  (20 + 16) / (10 + 16)   <   (15000 + 16) / (10000 + 16)

but

(ii)     20    /     10      >        15000   / 10000

You assume that measurements of 20 and 10 are less reliable (or perhaps 
biologically less important?) than measurements of 20000 and 10000, thus 
that ranking (i) should be used - but that depends on an error model 
(which you encode in the pseudocount parameter '16') and a subjective 
trade-off between precision and effect size.

I agree with you that the approach is useful, and also that it is good 
to provide a very simple recipe for people that either cannot deal with 
or do not care about the quantitative details. Still, this post is for 
the people that do :)

Cheers
	Wolfgang


>
> Best wishes
> Gordon
>
>
>> Date: Tue, 05 Apr 2011 18:05:08 +0200
>> From: "Seraya Maouche" <Seraya.Maouche at uk-sh.de>
>> To: <Bioconductor at r-project.org>
>> Subject: [BioC] Limma
>>
>> Dear Prof Gordon, dear Bioconductor members,
>>
>> I have performed gene expression analysis using Limma (Illumina human
>> ref8) comparing two types of cells (referred below as cond1 and cond2).
>> Based on detection call, I filtered out transcripts which are absent in
>> both types of cells. Transcripts which were expressed only in one cell
>> type were included in the analysis.
>>
>> I have received the comment below from a reviewer who seems not agree to
>> calculate fold change for genes expressed only in one condition. Would
>> it be possible to have your opinion about this.
>>
>> Thank you in advance for your time,
>> S Maouche
>>
>> "There is a little conceptual difficulty related to the cond1/cond2
>> comparisons for genes that are considered not detected. If a gene
>> product is absent (0) in one cell then no fold change can be computed
>> (table 2). I don?t know how to circumvent this difficult except by
>> saying that the ?noise? is considered to reflect low expression. The
>> terms ?not detected? and ?not expressed? are often used interchangeably
>> while this is not the same. Detection is based on the definition adopted
>> and in many places of the manuscript it should be used in place of
>> expression."
>>
>>
>>
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