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Question: error in getsymbol function
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gravatar for farahqureshi5
20 months ago by
farahqureshi50 wrote:

Greetings!!

i wnat to annotating the results with associated gene symbols but i am not getting an error

gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2")
           Error in unlist(lookUp(x, data, "SYMBOL")) :
            error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in lookUp(x,         data, "SYMBOL") : No keys provided

ADD COMMENTlink modified 20 months ago by Guido Hooiveld2.3k • written 20 months ago by farahqureshi50
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gravatar for Guido Hooiveld
20 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

Without providing more code it is rather difficult to help, but:

- the error message indicates that the object probeset.list$ID is empty.

- you are using an outdated interface to query annotation databases; you'd better either use select() or mapIds(). See ?select or ?mapIds after loading the library AnnotationDbi for more information on these functions.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Guido Hooiveld2.3k
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