Question

Error UseMethod ("select_"): from bioconductor dplyr select package

1

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abedini.jaleh ▴ 10

@abedinijaleh-14228

Last seen 6.9 years ago

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 dplyr select • 7.2k views

ADD COMMENT • link updated 7.1 years ago by Martin Morgan 25k • written 7.1 years ago by abedini.jaleh ▴ 10

Martin Morgan · Answer 1 · 2017-10-20

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

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

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

ADD COMMENT • link 7.1 years ago Martin Morgan 25k

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Thank you so much it worked

ADD REPLY • link 7.1 years ago abedini.jaleh ▴ 10

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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 REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by rgeysels • 0

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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 REPLY • link 5.4 years ago James W. MacDonald 67k