[BioC] Average expression value from limma

[Ekta Jain]

Dear Paul,
Thanks very much for your reply. My data is from rice and its an affymetrix array with 57,000 probes. The genes from limma show a high 'average expressio' for contrast of mock vs treated having 3 replicates in each group. When i do an average of the expression values of each of the three replicates from the gcrma normalised files, the value is much lower as compared to the one obtained from limma.

I am unable to understand why is this so maybe becauase i do not know how limma calculates this average.

Thank you,
Ekta


 -----Paul Geeleher <paulgeeleher at gmail.com> wrote: ----- 

 ======================= 
 To: Ekta Jain <Ekta.Jain at teri.res.in>
 From: Paul Geeleher <paulgeeleher at gmail.com>
 Date: 05/20/2013 07:37PM
 cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
 Subject: Re: [BioC] Average expression value from limma
 ======================= 

 Normally I think you'd expect that differentially expressed genes tend
to have higher average intensity. Consider that your array is
measuring approx 25,000 transcripts, this means that in your tissue
type many of these will not even be expressed, thus are highly
unlikely to be identified as differentially expressed. These probes
will obviously have the lowest flourescence intensity levels, thus
skewing the overall average flourescencce intensity level towards
zero.

On some platforms it is possible to identify and remove these probes,
for example if you're using Affymetrix Exon arrays you can apply the
DABG algorithm.

You'd probably still want to provide some info on how big the
difference is and what the array platform is though.

Paul.



On Mon, May 20, 2013 at 6:15 AM, Ekta Jain <Ekta.Jain at teri.res.in> wrote:
>
> Dear Bioconductor Mailing List,
> I have a microarray data which i normalised using 'gcrma' followed by limma
> for Mock vs Treated, 3 replicates in each group. The 'topTable' returns an
> average expression value for each probeset. How is this exactly calculated?
>
> Also i compared this with the average expression of each probeset for all
> samples, such as
> (Embedded image moved to file: pic17982.gif)
>
> The 'Avg.Expr.from.limma' has a very high value as compared to the ones
> obtained from the normalised data. Is there anything wrong?
>
> Much appreciate any comments please.
>
> Regards,
> Ekta Jain
> Research Analyst
> Biotechnology and Bio-resources Division
> The Energy and Resources Institute, India Habitat Centre
> Lodhi Road, New Delhi - 110033
> #09958818853
> ekta.jain at teri.res.in
>
>
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-- 
Dr. Paul Geeleher, PhD (Bioinformatics)
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
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