[BioC] general question about omogeneity of variances between microarray groups

[James W. MacDonald]

Hi Guido,

On 7/31/2012 5:13 AM, Guido Leoni wrote:
> Dear list
> I'm performing some microarrays analysis for a simple case(15 microarrays)
> , control(3 microarrays) experiment design.
> Don't ask me the reason for which i have a so unbalanced dataset ;-)
> In order to detect differentially expressed genes I wish to perform a LIMMA
> analysis...but checking the omogeneity of variances with bartlett test I
> observ a difference statistically significative between cases and controls.

If you are using limma, you will be shrinking your variance estimates 
towards an overall value, so I doubt that the unbalanced design will be 
a big concern.

> According to your experience:
> Is a good idea before doing a parametric analysis checking the variances
> utilizing Bartlett test?

That might be an issue if you are doing a handful of tests, but I don't 
see the applicability when you are doing thousands.

> In my case a non parametric test(like SAM) might be better than LIMMA?

SAM isn't non-parametric. The biggest difference between limma and SAM 
is that you are using permutation to construct a null distribution in 
the case of SAM, but you use a conventional t-distribution for limma. 
However, in both cases you are estimating parameters and comparing to a 
null distribution.

Best,

Jim


> thak you for any tips
> Best
> Guido
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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