[BioC] phenoTest and variable-wise multiple testing

[James W. MacDonald]

Hi Jon,

On 1/14/2013 7:07 AM, Jon Manning wrote:
> Hi Bioconductors,
>
> I'm using the phenoTest package to look for associations between 
> various continuous and categorical clinical variables and methylation 
> values stored in an eset-like object.
>
> As suggested I apply the BH method to correct for multiple testing 
> probe-wise. However, as I understand it this does not account for 
> variable-wise multiple testing, and with my collaborator introducing 
> many new variables I'm concerned this will create unnecessary spurious 
> associations.
>
> So the question is simple: should I just do a simple column 
> (variable)-wise bonferroni correction, after the row (probe) -wise BH 
> correction?

Adding more variables to the model doesn't increase the number of tests, 
but doing more tests does. In other words, if you are fitting multiple 
models, then you are increasing the number of tests, but simply adding a 
new variable to an existing model doesn't increase multiplicity (as long 
as you only use your final model).

Best,

Jim


>
> All pointers appreciated,
>
> Regards,
>
> Jon Manning
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099