ENSEMBL to ENTREZ ID
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@f7281b41
Last seen 3 months ago
United Kingdom

Hi there, I got a list of DEG from my scRNAseq from mouse.I would like to run some analysis using ClusterProfiler. However, I'm facing a problem that I'm unable to convert the ENSEMBL gene names to ENTREZ ID. Can you please help me with that? Below all information about the code and Error I'm getting.

Code should be placed in three backticks as shown below

> library("AnnotationDbi")
>library("org.Mm.eg.db")
>sigs.df<- as.data.frame (df3)

>sigs.df
                     X          Gene      pvalue log2FoldChange pct.1 pct.2        padj
1   ENSMUSG00000021270      Hsp90aa1 1.02894e-16     -1.0737909 0.524 0.832 3.19518e-12
2   ENSMUSG00000041859          Mcm3 1.34494e-14     -0.9469918 0.113 0.436 4.17644e-10
3   ENSMUSG00000041133         Smc1a 1.80664e-14     -0.7971461 0.262 0.621 5.61017e-10
4   ENSMUSG00000009575          Cbx5 3.55868e-14     -0.6508072 0.226 0.572 1.10508e-09
5   ENSMUSG00000022391       Rangap1 6.29202e-14     -0.7469614 0.107 0.415 1.95386e-09
6   ENSMUSG00000029623         Pdap1 2.24799e-13     -0.4088167 0.149 0.438 6.98068e-09
7   ENSMUSG00000029730          Mcm7 2.25639e-13     -0.3725229 0.161 0.448 7.00678e-09
8   ENSMUSG00000027715         Ccna2 4.19436e-13     -0.3656079 0.137 0.418 1.30248e-08
9   ENSMUSG00000028312          Smc2 4.55697e-13     -0.4142646 0.244 0.554 1.41508e-08
10  ENSMUSG00000032026         Rexo2 5.96883e-13     -0.6615188 0.060 0.325 1.85350e-08

> sigs.df$entrez <-mapIds(org.Mm.eg.db, keys = rownames(sigs.df), keytype="ENSEMBL", column = "ENTREZID")

Result from R:

sigs.df$entrez <-mapIds(org.Mm.eg.db, keys = rownames(sigs.df), keytype="ENSEMBL", column = "ENTREZID") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

sessionInfo( )

```

THanks a lot for your help

clusterProfiler • 386 views
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Guido Hooiveld ★ 3.4k
@guido-hooiveld-2020
Last seen 16 minutes ago
Wageningen University, Wageningen, the …

Please note that you are using keys = rownames(sigs.df) as input. These are 1, 2, 3 etc., and are obviously no valid ENSEMBL IDs. You rather should use as input sigs.df$X.

> library(org.Mm.eg.db)
> ids <- c("ENSMUSG00000021270", "ENSMUSG00000041859", "ENSMUSG00000041133")
> mapIds(org.Mm.eg.db, keys = ids, keytype="ENSEMBL", column = "ENTREZID")
'select()' returned 1:1 mapping between keys and columns
ENSMUSG00000021270 ENSMUSG00000041859 ENSMUSG00000041133 
           "15519"            "17215"            "24061" 
>
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Hi Guido,

many thanks for that. It has successfully solved the problem here. Thanks Best Marta

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