[R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

[Martin Morgan]

Are you remembering to attach the Biobase package to your R session?

> AnnotatedDataFrame()
Error in AnnotatedDataFrame() :
  could not find function "AnnotatedDataFrame"
> suppressPackageStartupMessages({ library(Biobase) })
> AnnotatedDataFrame()
An object of class 'AnnotatedDataFrame': none

Biobase is a Bioconductor package, so support questions should more appropriately go to https://support.bioconductor.org

Martin

On 7/17/19, 4:20 PM, "R-help on behalf of Spencer Brackett" <r-help-bounces using r-project.org on behalf of spbrackett20 using saintjosephhs.com> wrote:

    Good evening,
    
    I downloaded the Biobase package in order to utilize the ExpressionSet and
    other features hosted there to examine annotations for probeset data, which
    I seek to visualize. I currently have pre-analyzed object located in my
    environment containing said probeset info, along with gene id and location.
    After experimenting with the following approaches, I'm am at a loss for as
    to why the AnnotatedDataFrame function is not being recognized by R.
    
    ##Example of some of my attempts and their respective error messages##
    
    >AnnotatedDataFrame()
        Error in AnnotatedDataFrame() : could not find function
       "AnnotatedDataFrame"
    
     signature(object="assayData")
         object  "assayData"
    > annotatedDataFrameFrom("assayData", byrow=FALSE)
    Error in annotatedDataFrameFrom("assayData", byrow = FALSE) :
      could not find function "annotatedDataFrameFrom"
    
    >as(data.frame, "AnnotatedDataFrame")
    Error in as(data.frame, "AnnotatedDataFrame") :
      no method or default for coercing “function” to “AnnotatedDataFrame”
    
    Best,
    
    Spencer
    
    	[[alternative HTML version deleted]]
    
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