[BioC] Average expression value from limma

[Paul Geeleher]

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
>
>
> ------------------------------------------------------------------------------------------------------------
>
> Disclaimer:
>
> The information contained in this e-mail is intended f...{{dropped:26}}