Question: Too many fails converting gene SYMBOL to ENTREZID
gravatar for MatthewP
5 weeks ago by
MatthewP210 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

# convertion
gene_list <- bitr(expr_2$Gene_Symbol, fromType="SYMBOL", toType="ENTREZID",, drop=TRUE)

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

ADD COMMENTlink modified 4 weeks ago • written 5 weeks ago by MatthewP210

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

ADD REPLYlink written 4 weeks ago by Kevin Blighe47k

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

ADD REPLYlink written 4 weeks ago by MatthewP210
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