Hi all,

I used DESeq2 to do Pseudobulk analysis on my Seurat object. I have a problem converting gene names to Ensembl IDs. My row names are, some with ENSG, some with gene names. I want to have Ensembl IDs and chromosome names as well. Here is the part of my DESeq code for Pseudobulk analysis:

dds <- DESeqDataSetFromMatrix(countData = counts_bcell,
                              colData = colData,
                              design = ~Age+Sex+condition)

#filter
keep <- rowSums(counts(dds)) >=10
dds <- dds[keep,]

colData(dds)$condition <- relevel(colData(dds)$condition, ref = "Control")

#run DESeq2
dds <- DESeq(dds, test = "LRT", reduced = ~Age+Sex)


#check the coefficients for the comparison
resultsNames(dds)

#Generate result object
res <- results(dds, name = "condition_Patient_vs_Control")

mapped <- data.frame(GeneName = rownames(res),
                     ensemblID = mapIds(org.Hs.eg.db, keys =rownames(res), keytype = "SYMBOL", column="ENSEMBL"))

res$ensembl_gene_id <- mapped$ensemblID

If we look at mapped it looks like as below for the gene names with ENSG I don't get any ensemblID.

> mapped
                       GeneName       ensemblID
ENSG00000238009 ENSG00000238009            <NA>
ENSG00000241860 ENSG00000241860            <NA>
ENSG00000290385 ENSG00000290385            <NA>
ENSG00000291215 ENSG00000291215            <NA>
ENSG00000229905 ENSG00000229905            <NA>
LINC01409             LINC01409            <NA>
ENSG00000290784 ENSG00000290784            <NA>
FAM87B                   FAM87B ENSG00000177757
LINC00115             LINC00115            <NA>

Any suggestions, please, or a better way to add ensemblID and chromosome name and biotype?

I appreciate your help. Many thanks!

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I would use biomaRt.

This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output names of the alignment and quantification software used. For example if ensembl annotations were used, then all sample rows would have ensemble IDs.