[BioC] questions on results from mt.maxT (multtest)

[Straubhaar, Juerg]

Hi Adai,

The multtest version I am using is version 1.5.2 and the default value of B is 10000. Even if I set B to 100000 only 20 permutations will be calculated. I have two classes and 3 members in each class. The maximum number of permutations of the 6 columns (2 X 3) is 20. So how can I do 10000 permutations?

Juerg


-----Original Message-----
From: Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk]
Sent: Sun 2/13/2005 10:45 PM
To: Straubhaar, Juerg
Cc: BioConductor mailing list
Subject: Re: [BioC] questions on results from mt.maxT (multtest)
 
The resolution of your p-value by permutation test is 1/B where B is the
number of iterations. In the output shows, I think it says B=20. Thus
your resolution (or smallest p-value) is 1/20 = 0.05.

However I am wondering why did your function mt.maxT() default to B=20
when the current of multtest (1.5.2) has a default of B=10000 ?

Are you by any chance using a very old version of multtest ? If so, you
can try upgrading or explicitly set B=10000 (or something higher) in
mt.maxT. Otherwise check your inputs.

Regards, Adai


On Sun, 2005-02-13 at 13:02 -0500, Straubhaar, Juerg wrote:
> Im am using R version 2.0.1, multtest version 1.5.2.
> 
> Microarray experiment: wildtype tissue vs KO tissue; affy MOE430_2
> Experiments in triplicates.
> 
> ExprSet at exprs matrix has dimension: 45101 6
> 
> I used nonspecific filtering which reduces the number of genes to 1815 (exprSub)
> 
> I am using multtest to get a set of differentially expressed genes:
> 
> resT <-mt.maxT(exprSub at exprs, c(0,1,0,1,0))
> This runs 20 permutations (complete enumeration)
> 
> sort(resT$rawp) looks like this:
> 
> [1] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> [20] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> [39] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
> ...
> [1711] 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9
> [1729] 0.9 0.9 0.9 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1747] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1765] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1783] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> [1801] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> 
> It looks like these p-values are rounded to one decimal digit. From these results none of the 1815  genes are differentially expressed between WT and KO, which is not quite believable. I would like to get p-values precise to several digits. Maybe there is something else I don't understand.
> 
> getOption('digits') 7
> 
> Thank you.
> 
> Juerg Straubhaar
> Umass Med
> 
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