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Question: What is the name of this probe?
0
6 weeks ago by
sindre.lee0 wrote:

Hello, I have googled my self half to death, I cannot understand this:

select(hta20transcriptcluster.db, keys=featureNames(vv), columns=c("SYMBOL","GENENAME"), keytype="Ensemble")

Error in testForValidKeytype(x, keytype) :
Invalid keytype: Ensemble. Please use the keytypes method to see a listing of valid arguments.

My probes look like this:

[997] "TC0100013150.hg.1" "TC0100013155.hg.1" "TC0100013156.hg.1" "TC0100013158.hg.1"

I really cannot figure out that the "keytype" for these probes are.. Data are obtained by HTA-2.0. I know its not "Ensemble", but I have tried everything I can think of, and I just dont get it. Google has not helped and I have read every single thread on the internet the resembles this problem.

Nevermind! After hours of trial and error, i figured it was from the Clariom D Human Microarray CDF file to package. clariomdhumantranscriptcluster.db is the way to go.

modified 6 weeks ago by James W. MacDonald49k • written 6 weeks ago by sindre.lee0
Answer: What is the name of this probe?
0
6 weeks ago by
United States
James W. MacDonald49k wrote:

As a followup, you haven't answered your original question. The error says this:

Error in testForValidKeytype(x, keytype) :
Invalid keytype: Ensemble. Please use the keytypes method to see a listing of valid arguments.

Which is intended to be self explanatory, but you have to pay attention for it to be so. It says Invalid keytype: Ensembl. And if you look at the function call you used, you will see that you said keytype="Ensemble". Which A) isn't a thing (it's Ensembl, without the e at the end), and B) it needs to be all caps, which you would have found by following the rest of the error message, which was Please use the keytypes method to see a listing of valid arguments.

So if you follow the instructions (and yes I know this isn't the same array, but they are +/- all the same anyway, and this is for pedantic reasons, so it doesn't really matter).

> keytypes(hugene20sttranscriptcluster.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"  

You would have seen that the valid choice is ENSEMBL.