gravatar for Ranan Jyoti Sarma

7 hours ago by

Mizoram Univesity

I have added gene name and Entrez ID in my DESeq2 result.
The commands I have used are:

res$hgnc_symbol <- convertIDs(gsub("\..*","", row.names(res)), "ENSEMBL", "SYMBOL", org.Hs.eg.db)

res$entrezgene <- convertIDs(gsub("\..*","", row.names(res)), "ENSEMBL", "ENTREZID", org.Hs.eg.db)

resOrdered <- res[order(res$pvalue),]

After, checking the object resOrdered:

head(resOrdered)

I am getting like this:

     gene_id             stat               pvalue                 padj
                       <numeric>            <numeric>            <numeric>
  ENSG00000280228.1   -5.9096792673878 3.42774467723773e-09 1.53944643600176e-05
  ENSG00000225555.1  -5.88657749721615 3.94274922781857e-09 1.53944643600176e-05
  ENSG00000234616.7  -5.77542188212913 7.67605073778235e-09 1.99807600704475e-05
  ENSG00000058866.13 -4.88480635581578 1.03530552769589e-06  0.00163524543935493
  ENSG00000180152.3   -4.8645382294294 1.14724332367248e-06  0.00163524543935493
  ENSG00000244968.5  -4.84652440600431 1.25643137868224e-06  0.00163524543935493
                         hgnc_symbol  entrezgene
                          <character> <character>
  ENSG00000280228.1           NA          NA
  ENSG00000225555.1           NA          NA
  ENSG00000234616.7          JRK        8629
  ENSG00000058866.13        DGKG        1608
  ENSG00000180152.3           NA          NA
  ENSG00000244968.5     LIFR-AS1   100506495

Here, I am not getting some gene names and Entrez ID and it is showing NA.

I have aligned my data to GRCh38 (took GTF from same assembly) with STAR and count file were created using htseq-count.

What could be the reason of these. Please put your valuable suggestion how I should go forward with this?



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