[BioC] globaltest question

[Oosting, J. (PATH)]

On small groups the globaltest automatically uses permutation tests. You
can see in your result that in this case there are 210 permutations, and
all p-values will therefore be multiples of 1/210, with a minimum of
1/210(=0.0047619). You can force it to use a more gliding scale by using
the argument method="asymptotic".

Jan

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of mike Ad.
Sent: dinsdag 12 september 2006 16:23
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] globaltest question

Dear list,

I am new to use the "globaltest" packages (version "4.2.0"). I have 10
mouse arrays from two groups (control and treated). I tested them
against all the kegg pathways. The result looks stage to me because
among the 171 pathways tested, most of them have the identical p-value.
And that p-value is the smallest.
The code I used is listed, could someone help to tell me where went
wrong with my code?

Thanks!

/Mike

kegg<-as.list(mouse4302PATH2PROBE)

gtkegg<-globaltest(affy_expression, diagno, kegg) ##where the first
argument "affy_expression" is the affy expression data set I got by
using function "exprs()", each row is one affy probe and each column is
from one array.
## the second argument "diagno" is a vector containing 10 group names
("treated" or "control") for the 10 arrays and they are in the
corresponding order to the 10 columns in the expression data.

gtkegg<-sort(gtkegg)

#Just list the top 5 of the result, the P-value are identical, what's
wrong?
gtkegg[1:5]
Global Test result:
Data: 10 samples with 45101 genes; 5 pathways tested
Model: logistic
Method: All 210 permutations

      Genes Tested Statistic Q Expected Q sd of Q   P-value
00623    12     12      37.552     9.1318  9.2135 0.0047619
00440    47     47      13.010     3.3143  1.7585 0.0047619
00624    43     43      57.812     9.1819  8.2350 0.0047619
00625    19     19      71.404    12.6820 10.4620 0.0047619
00626    28     28      15.648     3.5587  2.2039 0.0047619

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