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

[Spencer Brackett]

I thought it successfully loaded after library(Biobase) but after
implementing your suggested I got the following....

Error in library(Biobase) : there is no package called ‘Biobase’

So to download it would I try to rerun with Debug? This is an option given
as part of the return



On Wed, Jul 17, 2019 at 4:37 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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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