[BioC] globaltest question

[mike Ad.]

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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