Entering edit mode
6.0 years ago
hrhki2015
▴
10
I'm working on the expression analysis of soybean. The expression was analyzed by RNA-seq with RStudio, but GO analysis with the software have the error.
The software was RStudio Version 1.1.442.
library(org.XX.xxx.db)
library(goProfiles)
x <- read.csv("induction.txt", header=TRUE, sep=",")
head(x, n=3)
name logFC logCPM PValue FDR
1 GLYMA01G26750 4.002202 7.114714 9.781341e-29 1.613378e-26
2 GLYMA14G05850 3.427588 6.409440 5.438084e-26 5.381890e-24
3 GLYMA02G17940 4.585453 2.839647 5.506072e-25 5.108602e-23
Above is all right. So next has a problem...
induction <- basicProfile(genelist=x$name, onto='ANY', level=2, orgPackage="org.XX.xxx.db")
if I submit the "MeSH.Gma.eg.db" instead of "org.XX.xxx.db", the software return
eval(parse(text = envirName)) with error.
Could you explain and write the R code for the analysis? Can't I use "MeSH.Gma.eg.db" for the GO analysis? If you know the GO analysis with a different way, please let me know.
I'm not still used to R..
Haru
I think WebGestalt would be useful for you, it translates gene sets to biological insights.