Globaltest Pathway analysis with a matrix

Question

I have a matrix with SAGE count data and i want to test for GO enrichment en Pathway enrichment. Therefore I want to use the globaltest in R. My data looks like this:

data_file

                   KI_1 KI_2 KI_4 KI_5 KI_6 WT_1 WT_2 WT_3 WT_4 WT_6
ENSMUSG00000002012  215  141  102  127  138  162  164  114  188  123
ENSMUSG00000028182   13    5   13   12    8   10    7   13    7   14
ENSMUSG00000002017  111   72   70  170   52   87  117   77  226  122
ENSMUSG00000028184  547  312  162  226  280  501  603  407  355  268
ENSMUSG00000002015 1712 1464  825 1038 1189 1991 1950 1457 1240  883
ENSMUSG00000028180 1129  944  766  869  737 1223 1254  865  871  844

The rownames contains ensembl gene IDs and each column represent a sample. These samples can be divided in two groups for testing pathway enrichment: KI1 and the WT2 group

 groups <- c("KI1","KI1","KI1","KI1","KI1","WT2","WT2","WT2","WT2","WT2")

I found the function gtKEGG to do the pathway analysis, but my question is how? Because when I run the function I don't create any error but my output file is like this:

> gtKEGG(groups, t(data_file), annotation="org.Mm.eg.db")
  holm                                                      alias p-value Statistic Expected Std.dev #Cov
00380   NA                                      Tryptophan metabolism      NA        NA       NA      NA    0
01100   NA                                         Metabolic pathways      NA        NA       NA      NA    0
02010   NA                                           ABC transporters      NA        NA       NA      NA    0
04975   NA                               Fat digestion and absorption      NA        NA       NA      NA    0
04142   NA                                                   Lysosome      NA        NA       NA      NA    0
04012   NA                                     ErbB signaling pathway      NA        NA       NA      NA    0
04110   NA                                                 Cell cycle      NA        NA       NA      NA    0
04360   NA                                              Axon guidance      NA        NA       NA      NA    0

Can anyone help me with this question? Thanks! :)

You might have better luck asking on the Bioconductor mailing list. — joran

Lisann Lisann · Accepted Answer · 2012-04-23T06:32:02

I found the solution!

library(globaltest)
library(org.Mm.eg.db)

eg <- as.list(org.Mm.egENSEMBL2EG)
KEGG<-gtKEGG(as.factor(groups), t(data_file), probe2entrez= eg, annotation="org.Mm.eg.db")

Globaltest Pathway analysis with a matrix

1 Answers