[BioC] Intra variance Vs inter group variance: scared!

[James W. MacDonald]

Hi Emmanuel,

Emmanuel Levy wrote:
> Dear All,
> 
> I've got two conditions and three replicates per condition:
> A1 A2 A3 B1 B2 B3
> 
> To test the INTRA VS INTER group variance, I compared the fold changes
> within group and between groups:
> 
> length(which(A1/A2 > 5))=686
> length(which(A1/B1 > 5))=708
> 
> The fact that this is similar is quite scary! What do you think?

Scary? No. I do think it illustrates why Statisticians recommend doing 
replicates rather than relying on fold change for assessing differential 
expression. It is quite possible that the 686 genes that have a fold 
change greater than 5 are just noisy in general, so if you use a 
statistic that accounts for the intra-sample variance these genes will 
likely not end up being significant. It is also possible that these data 
are Just Not Good(tm).

I presume you have done some other exploratory data analysis designed to 
tell if the data are bad or not?

> 
> Do you know of a package that would show somehow that the noise found above
> should not prevent me from getting meaningful results with these data?

It depends on the platform. However, there are many packages on this 
page designed for assessing the quality of your data:

http://www.bioconductor.org/packages/1.9/Visualization.html

Best,

Jim



> 
> Many thanks in advance for your help,
> 
> Emmanuel
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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