Entering edit mode
5.0 years ago
ddzhangzz
▴
90
Suppose all of log2 fold changes from 1000 genes are negative (down regulated)
library(gage)
go.set <- go.gsets(species = "human")
go.cc.hs <-go.set$go.sets[go.set$go.subs$CC]
fcs<- -c(1:1000)
set.seeds(123)
names(fcs)<-sample(unlist(go.cc.hs), 1000)
head(fcs)
7392 10139 26470 91039 170575 214
-1 -2 -3 -4 -5 -6
x<-gage(fcs, go.cc.hs)
head(x[["greater"]])
p.geomean stat.mean
GO:0035770 ribonucleoprotein granule 0.01073012 2.423047
GO:0036464 cytoplasmic ribonucleoprotein granule 0.01816832 2.195199
GO:0005770 late endosome 0.07821994 1.437179
GO:0044440 endosomal part 0.08148658 1.404548
GO:0005844 polysome 0.08386275 1.439267
GO:0019867 outer membrane 0.08875160 1.386214
p.val q.val set.size
GO:0035770 ribonucleoprotein granule 0.01073012 0.7266728 17
GO:0036464 cytoplasmic ribonucleoprotein granule 0.01816832 0.7266728 16
GO:0005770 late endosome 0.07821994 0.7266728 28
GO:0044440 endosomal part 0.08148658 0.7266728 56
GO:0005844 polysome 0.08386275 0.7266728 10
GO:0019867 outer membrane 0.08875160 0.7266728 14
exp1
GO:0035770 ribonucleoprotein granule 0.01073012
GO:0036464 cytoplasmic ribonucleoprotein granule 0.01816832
GO:0005770 late endosome 0.07821994
GO:0044440 endosomal part 0.08148658
GO:0005844 polysome 0.08386275
GO:0019867 outer membrane 0.08875160
Since all fold changes are negative, I am wondering how the "greater" pathways have been calculated?
Short answer would be read the manuals and related papers, (there are other papers cited in the manuals, check them out, too).
There is no answer for this question in the manual.