[BioC] phenoTest and variable-wise multiple testing

[Jon Manning]

Hi Jim,

Thanks very much for the reply.

phenoTest looks for univariate assocations- i.e. it tests variables 
one-by-one using Limma, so in this case I have many tests and I guess I 
will have to correct appropriately.

Regards,

Jon



On 14/01/2013 15:09, James W. MacDonald wrote:
> 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
>>
>

-- 
Dr Jonathan Manning
Bioinformatics Team
Centre for Cardiovascular Science
University of Edinburgh
Queens Medical Research Institute
47 Little France Crescent
Edinburgh  EH16 4TJ
United Kingdom
T: +44 131 242 6700
F: +44 131 242 6782
E: jmanning at staffmail.ed.ac.uk


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