bitr() doesn't recognize the keys I've entered as valid gene symbols for my organism's database ('SYMBOL').

Question

[Medeea]

Hello,

In trying to re-run my pathway analysis with a DEG set annotated with gene symbols. I have encountered this error while wanting to retrieve Entrez IDs for clusterProfiler. This is a new error, as I have worked with the same script before.

up.genes.entrez <- clusterProfiler::bitr(up.genes,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Hs.eg.db)
Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.

I can not figure out why keytype SYMBOL are not recognized as valid gene symbols anymore. I have tried reinstalling or updating the packages and I would be most grateful for additional suggestions.

[Trivas]

Can you look at your db file? Sometimes symbol is hgnc_symbol.

[Basti]

Please share a reproducible example, we need to know what is up.genes

Answer 1

[Basti]

up.genes should be a vector of gene IDs whereas in your case, up.genes is a tibble with one column.

You should select the column of geneIDs and not the tibble :

up.genes.entrez <- clusterProfiler::bitr(up.genes$Symbol,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Hs.eg.db)

up.genes.entrez
   SYMBOL ENTREZID
1  CCL3L3   414062
2   F13A1     2162
3 ANGPTL4    51129
4    THBD     7056
5    SYN2     6854
6   CXCL3     2921

[Medeea]

Yes, you are correct. It works now, thank you so much!

Answer 2

[Medeea]

I extract the list of genes from my DEG data set:

head(DEG)

A tibble: 6 × 8

Gene Id` baseMean log2FoldChange lfcSE stat pvalue padj Symbol
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
1 6373 67.7 -2.32 0.310 -7.50 6.28e-14 1.69e-12 CXCL11

up.genes <- DEG[DEG$log2FoldChange > 1 & DEG$padj < 0.05, 8] head(up.genes)

A tibble: 6 × 1

Symbol <chr>
1 CCL3L3 2 F13A1
3 ANGPTL4 4 THBD
5 SYN2
6 CXCL3

There after, with clusterProfiler::bitr(), I would have another column with EntrezID that clusterProfiler::enrichGO() will want in order to do the pathway analysis. Before it worked for several analysis, and now that I am using it again I get this error.

Thank you!