gage function problem in R
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eozcan • 0
@eozcan-22798
Last seen 5 months ago
United States

I did RNA-seq analysis using DESeq2. Got the results and want to draw a Kegg pathway with the enriched gene sets. So, I am trying to use gage function.

I followed the instructions in the manual and got to exp.fc as below: head(exp.fc) lp0001 lp0002 lp0004 lp0005 lp0006 lp0007 -0.3297675 0.2703983 -0.1043349 -0.4814408 1.2165759 -0.3020035

and then I extracted genesets using kegg.gsets(species ="lpl", id.type = "kegg", check.new=FALSE). this is my output

head(gsets) $kg.sets $kg.sets$lpl00010 Glycolysis / Gluconeogenesis [1] "lp0082" "lp0330" "lp0350" "lp0440" "lp0537" "lp0597" "lp0764" "lp0789" "lp0790" [10] "lp0791" "lp0792" "lp0826" "lp0884" "lp0906" "lp1101" "lp1245" "lp1401" "lp1573" [19] "lp1665" "lp1731" "lp1897" "lp1898" "lp1920" "lp2151" "lp2152" "lp2153" "lp2154" [28] "lp2349" "lp2502" "lp2777" "lp2778" "lp2873" "lp3008" "lp3011" "lp3132" "lp3170" [37] "lp3418" "lp3487" "lp3512" "lp3520" "lp3525" "lp3526" "lp3629" "lp3662"

So my gsets have the same id as my exp.fc. However when I apply gage function, fc.kegg.p <-gage(exp.fc, gsets = gsets, ref = NULL, samp = NULL)

my fc.kegg.p is all NAN as below: head(fc.kegg.p) $greater p.geomean stat.mean p.val q.val set.size exp1 kg.sets NA NaN NA NA 3 NA sigmet.idx NA NaN NA NA 0 NA sig.idx NA NaN NA NA 0 NA met.idx NA NaN NA NA 0 NA dise.idx NA NaN NA NA 0 NA

$less p.geomean stat.mean p.val q.val set.size exp1 kg.sets NA NaN NA NA 3 NA sigmet.idx NA NaN NA NA 0 NA sig.idx NA NaN NA NA 0 NA met.idx NA NaN NA NA 0 NA dise.idx NA NaN NA NA 0 NA

$stats stat.mean exp1 kg.sets NaN NA sigmet.idx NaN NA sig.idx NaN NA met.idx NaN NA dise.idx NaN NA

I saw some suggestions as using ENTREZ ID. but the IDs are matching in both kg.sets and my exp.fc. there is one thing that I cannot figure out how gage does not match it. are the IDs really the problem? or is there something that I miss?

gage R kegg pathview • 194 views
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