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Question: Error in columns(org.Hs.eg.db) : could not find function "columns"
0
gravatar for Sanches
8 days ago by
Sanches0
Sanches0 wrote:

Hi all, 

I have been running an analysis from microarray data and when I try to run this line " columns(org.Hs.eg.db)", I get an error. Could anyone please help me to understand this problem?

 

source("https://bioconductor.org/biocLite.R")
install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/data/annotation")
biocLite("org.Hs.eg.db")
biocLite("hgu95av2.db")
biocLite("tidyverse")
columns(org.Hs.eg.db)
keytypes(org.Hs.eg.db)

Thanks in advance

ADD COMMENTlink modified 8 days ago by James W. MacDonald44k • written 8 days ago by Sanches0
1

Please edit your question to show the error and the output of your sessionInfo().

ADD REPLYlink written 8 days ago by Valerie Obenchain ♦♦ 6.2k
2
gravatar for James W. MacDonald
8 days ago by
United States
James W. MacDonald44k wrote:

There are two problems here. First, don't do this:

install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/data/annotation")

The whole idea behind biocLite is that you don't need to figure out what repository to use, particularly since Bioconductor package versions are specific to a given R version. By hijacking the process like that you are taking the chance that you will install the wrong thing.

Second, you have to load a package before you can use it.

> columns(org.Hs.eg.db)
Error in columns(org.Hs.eg.db) : could not find function "columns"
> library(org.Hs.eg.db)

<snip>

> columns(org.Hs.eg.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] "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"       "UNIGENE"     
[26] "UNIPROT"    
ADD COMMENTlink written 8 days ago by James W. MacDonald44k

Hi James, 

Thanks for your help.

I had loaded the package before using "columns".

I  have found out the problem. Everything went well when I loaded the biomaR package.

Thanks

 

 

 

 

ADD REPLYlink written 7 days ago by Sanches0
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