[BioC] Cutoff for non-specific gene filtering?

[Suraj Menon]

Thank you Robert and Sean.
That makes much more sense!
Cheers
-Suraj

Suraj Menon
PhD Student
Department of Pathology
Henry Wellcome Building
School of Medicine
Cardiff University
Heath Park
Cardiff CF14 4XN

Tel:    +44 29 2074 3979
Email: MenonS1 at Cardiff.ac.uk
>>> Robert Gentleman <rgentlem at fhcrc.org> 30/04/08 10:50 PM >>>


Suraj Menon wrote:
> Hi all
> 
> Am curious to know why the recommended cutoff to remove non-variable genes is an IQR of 0.5.
> What is the significance of this number?

Hi,
  It is the median (not the value of the IQR), so you are taking the top 
.5 (by variability). A bug in an early version used the number directly, 
but this has long since been found and fixed.

> Also, why use IQR as opposed to any other measure of variability, like SD?

   Use what ever you want.  IQR tends to be more robust to outliers, 
which at least at one time were somewhat prevalent in gene expression 
studies (they are less so now as all relevant technologies have improved).

  best wishes
    Robert

> 
> Cheers
> -Suraj
> 
> Suraj Menon
> PhD Student
> Department of Pathology
> Henry Wellcome Building
> School of Medicine
> Cardiff University
> Heath Park
> Cardiff CF14 4XN
> 
> Tel:    +44 29 2074 3979
> Email: MenonS1 at Cardiff.ac.uk
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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rgentlem at fhcrc.org