bigmw,
Thanks a lot for your quick answer!
I have solved the problem, because GeneID is in column2.
>names(edger.fc) = test$GeneID
> head(exp.fc)
409677 100576979 100577819 552035 413550 413908
5.557823 4.667221 4.516693 4.127615 3.986429 3.937341
The first line is GeneID, and the second line is logFC.
Now I met another problem that the geneset file of kegg.gs could not be used for honey bee, because I could not run the following command:
> pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid, species ="ame", out.suffix = out.suffix))
Then I checked the fc.kegg.p$greater, I got the following results.
> head(fc.kegg.p$greater)
hsa00010 Glycolysis / Gluconeogenesis NA NaN NA
hsa00020 Citrate cycle (TCA cycle) NA NaN NA
hsa00030 Pentose phosphate pathway NA NaN NA
hsa00040 Pentose and glucuronate interconversions NA NaN NA
hsa00051 Fructose and mannose metabolism NA NaN NA
hsa00052 Galactose metabolism NA NaN NA
q.val set.size exp1
hsa00010 Glycolysis / Gluconeogenesis NA 0 NA
hsa00020 Citrate cycle (TCA cycle) NA 0 NA
hsa00030 Pentose phosphate pathway NA 0 NA
hsa00040 Pentose and glucuronate interconversions NA 0 NA
hsa00051 Fructose and mannose metabolism NA 0 NA
hsa00052 Galactose metabolism NA 0 NA
The kegg.gs file seems for anaysis of human genes.
What genesets files can I use for honeybee genes, and If there is not any available, How can I create one by myself from the kegg pathway files?
Have a good weekend!
Richard
Thanks a lot for your quick answer!
I have solved the problem, because GeneID is in column2.
>names(edger.fc) = test$GeneID
> head(exp.fc)
409677 100576979 100577819 552035 413550 413908
5.557823 4.667221 4.516693 4.127615 3.986429 3.937341
The first line is GeneID, and the second line is logFC.
Now I met another problem that the geneset file of kegg.gs could not be used for honey bee, because I could not run the following command:
> pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid, species ="ame", out.suffix = out.suffix))
Then I checked the fc.kegg.p$greater, I got the following results.
> head(fc.kegg.p$greater)
hsa00010 Glycolysis / Gluconeogenesis NA NaN NA
hsa00020 Citrate cycle (TCA cycle) NA NaN NA
hsa00030 Pentose phosphate pathway NA NaN NA
hsa00040 Pentose and glucuronate interconversions NA NaN NA
hsa00051 Fructose and mannose metabolism NA NaN NA
hsa00052 Galactose metabolism NA NaN NA
q.val set.size exp1
hsa00010 Glycolysis / Gluconeogenesis NA 0 NA
hsa00020 Citrate cycle (TCA cycle) NA 0 NA
hsa00030 Pentose phosphate pathway NA 0 NA
hsa00040 Pentose and glucuronate interconversions NA 0 NA
hsa00051 Fructose and mannose metabolism NA 0 NA
hsa00052 Galactose metabolism NA 0 NA
The kegg.gs file seems for anaysis of human genes.
What genesets files can I use for honeybee genes, and If there is not any available, How can I create one by myself from the kegg pathway files?
Have a good weekend!
Richard
Comment