problem faced in generating GSEA plot in R
0
0
Entering edit mode
4 months ago
bookorg ▴ 10

Hello, I have analysed three dataset and found 3 common DEG among them.But when i go for the GSEA analysis and try to draw the plot ,there I faced a trouble .When i run it,in return i get the bellow messages in R.I am very much confused about that.

preparing geneSet collections... GSEA analysis... no term enriched under specific pvalueCutoff... Warning message: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : All values in the stats vector are greater than zero and scoreType is "std", maybe you should switch to scoreType = "pos".

Here is my code:

library(readr)
sign_DEG_ <- read_csv("For GSEA,ORA,Pathway analysis/sign_DEG.csv")
View(sign_DEG)
library(dplyr)
library(stringr)
library(ggplot2)
library(ggpubr)
library(clusterProfiler)
library(ReactomePA)
library(org.Hs.eg.db)
library(EnsDb.Hsapiens.v86)
library(enrichplot)

geneid <- sign_DEG$SYMBOL

genes <- ensembldb::select(org.Hs.eg.db, 
                           keys=geneid, 
                           columns=c("ENTREZID"),
                           keytype="SYMBOL")

genes <- na.omit(genes)

sign_DEG <- merge(genes, sign_DEG, by = 'SYMBOL')

write.csv(sign_DEG_,"./Sign DEG after omit.csv", row.names = TRUE)

sign_DEGLogFC <- sign_DEG$logFC

names(sign_DEGLogFC) <-sign_DEG$ENTREZID

sign_DEG <- sort(sign_DEG, decreasing = TRUE)

bpSars <- gseGO(sign_DEGLogFC,
                ont = 'BP',
                org.Hs.eg.db)

bpSars <- setReadable(bpSars, org.Hs.eg.db)
bpSars@result$Description <- str_to_title(str_wrap(bpSars@result$Description, 50))

write.csv(bpSars, './Result/gsea-bp-sars.csv')
dotplot(bpSars, showCategory=10, split=".sign") + facet_grid(.~.sign)
ggsave('./Result/gsea-bp-sarscov.tiff', height = 8, width = 8)
GSEA ORA • 739 views
ADD COMMENT
0
Entering edit mode

Can you include your code?

ADD REPLY
0
Entering edit mode

it means there are no significantly differentially expressed genes (nothing statistically significant). Most immediately, I'd do two things:

1) set my p-value cut-off very liberally to see if this fixes the problem

2) set the scoreType argument to pos as they are suggesting.

If you still get errors after that, then maybe post those

ADD REPLY
0
Entering edit mode

according to your two points i got the 1st one but I am confused about the second point.Can you plz explain the second point in deeply plz.

ADD REPLY

Login before adding your answer.

Traffic: 918 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6