Question: Question about BiocManager and genefilter package
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gravatar for jkuhndechizelle
12 days ago by
jkuhndechizelle0 wrote:

Hi all, I need to use the BiocManager and genefilter package for one of my classes and cannot get the program to load in R. I was redirected to this website for answers.Below is the code and my errors. How do I fix this?:

> install.packages("BiocManager")
> BiocManager::install("genefilter")
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'genefilter'
Warning: package ‘genefilter’ is in use and will not be installed
Installation path not writeable, unable to update packages: boot, foreign,
  KernSmooth, mgcv, nlme
> library(genefilter)
> tt <- colttests(x, y)
Error in colttests(x, y) : object 'x' not found
software error • 56 views
ADD COMMENTlink modified 12 days ago by Martin Morgan ♦♦ 24k • written 12 days ago by jkuhndechizelle0
Answer: Question about BiocManager and genefilter package
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gravatar for Martin Morgan
12 days ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

The command

> library(genefilter)
>

completes successfully, indicatingt that genefilter has been loaded from from your library and attached to the current session. The command

> tt <- colttests(x, y)
Error in colttests(x, y) : object 'x' not found

indicates that you have tried to use colttests() from the genefilter package. R has found the function (in the genefilter package that you have attached to the current session) but has not found an object x, presumably because you have not defined x in your session. What x should be is defined on the help page ?colttests and you must figure out how to define it in a way relevant to your data.

ADD COMMENTlink written 12 days ago by Martin Morgan ♦♦ 24k
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