Question: Error UseMethod ("select_"): from bioconductor dplyr select package
1
gravatar for abedini.jaleh
2.1 years ago by
abedini.jaleh10 wrote:

I am running this code using the rat database

select(rat2302.db, PROBES, "ENTREZID")

to look in the rat database and get the  ENTREZID with the probes I extracted before.

and this error pops

Error in USEMethod("select_"):

no application method for 'select_' applied to an object of clad "c('ChipDB', 'AnnotationDb', 'envaRefClass', '.environment', 'refClass', 'environment' , refObject', 'AssayData')"

I tried this on both R version 3.4.1 and 3.3-PreUgrade and I could only make it work once it the pre-ugrade, but the error appeared again upon using it in a function. Now the code doesn't run at all.

I reinstalled Bioconductor and all the libraries and still have the same issue.

 

Does anybody knows what else I need to do?

 

bioconductor select dplyr • 1.8k views
ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 24k • written 2.1 years ago by abedini.jaleh10
Answer: Error UseMethod ("select_"): from bioconductor dplyr select package
3
gravatar for Martin Morgan
2.1 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Make sure that you're using the correct generic, from AnnotationDbi rather than dplyr

AnnotationDbi::select(rat2302.db, PROBES, "ENTREZID")

 

ADD COMMENTlink written 2.1 years ago by Martin Morgan ♦♦ 24k

Thank you so much it worked

ADD REPLYlink written 2.1 years ago by abedini.jaleh10

Hi, i'm having the same problem as abedini.jaleh:

>keytypes(hgu133plus2.db)
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "MAP"          "OMIM"        
[16] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"        
[21] "PROBEID"      "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"      
[26] "UNIGENE"      "UNIPROT"     

> mapAffy_Symbol <- select(hgu133plus2.db, rownames(data1), c("SYMBOL"))
Error in UseMethod("select_") : 
  no applicable method for 'select_' applied to an object of class "c('ChipDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"

and i can not solve it by using that code above:

*AnnotationDbi::select(rat2302.db, PROBES, "ENTREZID")*

>AnnotationDbi::select(hgu133plus2.db, PROBEID, "SYMBOL")
Error in .testForValidKeys(x, keys, keytype, fks) : 
  object 'PROBEID' not found

The problem is actually with hgu133plus2.db , i don't know if this has something to see with that database particularly or it's happening for everyone.

Is there any other solution for this? Or maybe there is something missing in my code Thank you for any help in advance!

Romina

ADD REPLYlink written 5 months ago by rgeysels0

Don't piggyback on ancient questions; instead submit a new question.

The error arises because PROBEID without quotes in R is assumed to be an object, which R is telling you it can't find. The second argument for select is supposed to be a character vector of keys that you are trying to look up, so unless you have a character vector called PROBEIDS, that won't work.

ADD REPLYlink written 5 months ago by James W. MacDonald51k
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