Hi ,
I am a  user of Sigpathway package(
http://www.chip.org/~ppark/Supplements/PNAS05.html).But i always get the
opposite result. That is,gene sets of negative NTk Stat are actually up
regulated ones,so for positive NTK stat .I found this when i compare the
results to that of by GSEA (http://www.broad.mit.edu/gsea/)

I check the phenotype twice,but i can not find any problems.

>cluster
  [1]  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  2  2  2  2  2
2  2  2  2  2  2  2  2  3  3  3  3  3  3  3  3
 [40]  3  3  3  3  3  3  3  3  3  3  3  4  4  4  4  4  4  4  4  4  4  4  4
4  4  4  5  5  5  5  5  5  5  5  5  5  5  5  5
 [79]  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5
5  5  5  5  5  5  5  5  6  6  6  6  6  6  6  6
[118]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  8  8  8  8  8
8  8  8  8  8  8  8  8  9  9  9  9  9  9  9  9
[157]  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9 10 10 10 10 10 10 10 10
10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11
[196] 11 11 11 11 11 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12
12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13
[235] 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14 15 15 15 15
15 15 15 15 16 16 16 16 16 16 16 16 16 16 16 17
[274] 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 19 19 19 19 19
>nn=19
>tab=unique.s
>phenotype=cluster
>phenotype[cluster==nn]=1
>phenotype[cluster!=nn]=0
>probeID=dimnames(tab)[[1]]
>gsList <- selectGeneSets(GS, probeID, 20, 500)
>nsim <- 1000
>ngroups <- 2
>verbose <- TRUE
>weightType <- "constant"
>methodNames <- c("NTk", "NEk")
>npath = 100
>allpathways <- FALSE

So what's the problem?

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