I am trying to get a KEGG pathway heat map with this python script
https://github.com/ajmazurie/color-KEGG-pathways/blob/master/README.rst

Till now I get this script but KEGG does find entrez id in the pathway from
my list.

#Get a list from genes in KEGG pathway in the expressionSet eset.LWT
probeids <- get("04010", mouse4302PATH2PROBE)
names.MAPK <- intersect(probeids,featureNames(eset.LWT))

#Select only the genes differentially expressed by limma contrast matrix
names.MAPK.selected_WT <- intersect(liver_WT.list$ID, names.MAPK)

#Get a table with fold change values from selected genes in the KEGG
pathway
MAPK <- liver_WT.list[ which(names.MAPK.selected_E %in%
liver_E.list$ID),1:2]

#Add Entrez ID
MAPK$ENTREZ<-unlist(as.list(mouse4302ENTREZID[MAPK$ID]))
MAPK<-MAPK[!is.na(MAPK$ENTREZ),]
MAPK<-MAPK[!duplicated(MAPK$ENTREZ),]

write.table(MAPK, "MAPK_WT.txt", sep="\t", quote=FALSE)

Could you help me to get an input for color-KEGG-pathways?

R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Spanish_Mexico.1252  LC_CTYPE=Spanish_Mexico.1252
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Mexico.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] mouse4302.db_2.7.1   org.Mm.eg.db_2.7.1   RSQLite_0.11.1
[4] DBI_0.2-5            AnnotationDbi_1.18.0 limma_3.12.0
[7] affy_1.34.0          Biobase_2.16.0       BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] affyio_1.24.0         BiocInstaller_1.4.4   IRanges_1.14.2
[4] preprocessCore_1.18.0 stats4_2.15.0         tools_2.15.0
[7] zlibbioc_1.2.0

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