Question: Too many fails converting gene SYMBOL to ENTREZID
0
gravatar for MatthewP
11 months ago by
MatthewP660
China
MatthewP660 wrote:

Hello, my dataset is GSE37133. I use GPL information to annotate gene SYMBOL(No bioconductor package for this chip). Main code:

gpl <- getGEO("GPL2996", destdir=".")
# dataframe that can map probes id and gene SYMBOL
annot <- Table(gpl)[,c(1, 2, 5, 10)]
# expression data annotation
expr_2 <- merge(x = annot, y = diff_expr_tenmg, by = "ID")

I want to call enrichKEGG function in clusterProfiler which do not support gene SYMBOL. So I need to run bitr to convert gene SYMBOL to ENTREZID. Main code

# load genowide annotation database
library(org.Rn.eg.db)
library(clusterProfiler)

# convertion
gene_list <- bitr(expr_2$Gene_Symbol, fromType="SYMBOL", toType="ENTREZID", OrgDb=org.Rn.eg.db, drop=TRUE)

Here, about 30% gene SYMBOL fails at converting. Where am I wrong? Thanks.

ADD COMMENTlink modified 11 months ago • written 11 months ago by MatthewP660

Your code is not reproducible because diff_expr_tenmg was never instantiated (?). Have you triied biomaRt to convert the gene symbols?

ADD REPLYlink written 11 months ago by Kevin Blighe61k
1

Sorry I didn't paste all my code here. I will try biomaRt later. Thanks Kevin.

ADD REPLYlink written 11 months ago by MatthewP660
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