How to get gene symbol after deseq?

[fabrice]

Dear experts,

After I have run deseq, I got a list of genes. They are something like as follow.

> resSig[,1]
[1] "ENSMUSG00000022150+ENSMUSG00000079102:009"
[2] "ENSMUSG00000026727:016"
[3] "ENSMUSG00000026727:004"
[4] "ENSMUSG00000022150+ENSMUSG00000079102:015"
[5] "ENSMUSG00000025730:010"
[6] "ENSMUSG00000005836:007"
[7] "ENSMUSG00000073139:001"

How can I get back the gene symbol for each ID?

Thank you very much in advance.

[thanhhoang]

Hi,
When counting mapped reads using HTseq, you need to use gene symbol insteads of gene_id (this is default)

[santhilalsubhash]

Use merge with your annotation and edgeR or DESeq result files.

Dear experts,

After I have run deseq, I got a list of genes. They are something like as follow.

> resSig[,1]
[1] "ENSMUSG00000022150+ENSMUSG00000079102:009"
[2] "ENSMUSG00000026727:016"
[3] "ENSMUSG00000026727:004"
[4] "ENSMUSG00000022150+ENSMUSG00000079102:015"
[5] "ENSMUSG00000025730:010"
[6] "ENSMUSG00000005836:007"
[7] "ENSMUSG00000073139:001"

How can I get back the gene symbol for each ID?

Thank you very much in advance.

If you have annotation file you can try merging the columns using column names.

I have also attached sample input and sample output files.


dbs <- read.table("sample_annotation.txt", header=TRUE)
resR <- read.table(edgeR_results.txt,header=TRUE)
newy <- cbind(rownames(resR),resR)
colnames(newy)[1] <- "ID"
annotated <- merge( dbs, newy, by='ID')
write.table(annotated,edgeR_results_annotated.txt,sep=" \t")

I hope this will help you.