Question: (Closed) Pathview error: no applicable method for 'select_'
1
gravatar for giuseppe0525
2.0 years ago by
giuseppe052520
Shanghai
giuseppe052520 wrote:

I came across a problem when trying to run pathview() to map gene expression data to KEGG.

1. I run this code:

pathview(gene.data = gene_matrix, 
         pathway.id = "04070", 
         species = "mouse")

The structure of the input object gene_matrix is shown as followed:

head(gene_matrix)
    497097      27395      21399     240690     319263      71096 
 0.6876964  0.4142183  1.4401079 -1.0009338  0.4017501  0.7701214

I got this error:

Error in UseMethod("select_") : 
  **no applicable method for 'select_' applied to an object of class "c('OrgDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"**
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "",  : 
  replacement has 29 rows, data has 49

2. The environment where I run the program was rstudio-server, which was installed on Cent OS 7 and R version was 3.4.4.

Detailed information is listed below:

> R.Version()
$platform
[1] "x86_64-redhat-linux-gnu"
$arch
[1] "x86_64"
$os
[1] "linux-gnu"
$system
[1] "x86_64, linux-gnu"
$status
[1] ""
$major
[1] "3"
$minor
[1] "4.4"
$year
[1] "2018"
$month
[1] "03"
$day
[1] "15"
$`svn rev`
[1] "74408"
$language
[1] "R"
$version.string
[1] "R version 3.4.4 (2018-03-15)"
$nickname
[1] "Someone to Lean On"

3. What puzzled me was that there seemed to be no problem with the pathview package, because I tested it with the demo data and the pathview() function worked well.

I run this code:

library(pathview)
data(gse16873.d)
pv.out <- pathview(gene.data = gse16873.d[, 1], 
                   pathway.id = "04110",
                   species = "hsa", 
                   out.suffix = "gse16873")

'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/**/R/**/**
Info: Writing image file hsa04110.gse16873.png

In addition, both the codes I run above (in green) worked well on RStudio built on Win 10.

The result of the first code is shown below:

pathview(gene.data = gene_matrix, 
          pathway.id = "04070", 
          species = "mouse")
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/**/R/**
Info: Writing image file mmu04070.pathview.png
There were 50 or more warnings (use warnings() to see the first 50)

The version of RStudio is 1.1.423 and the version of R is 3.4.2.

I really appreciate any help you offer. Thanks.

rna-seq R software error • 2.2k views
ADD COMMENTlink modified 2.0 years ago by zx87549.2k • written 2.0 years ago by giuseppe052520
1

Maybe the culprit is dplyr?

Please use the CODE FORMATTING button, your question is really hard to read due to the mix of code and regular text.

code_formatting

ADD REPLYlink written 2.0 years ago by h.mon29k

Thank you so much for your suggestion, which really solved the problem. It's the first time I have posted on Biostars.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by giuseppe052520
1

Thank zx8754 for editing your post, he did the hard work.

ADD REPLYlink written 2.0 years ago by h.mon29k
1

Hello giuseppe0525!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.0 years ago by zx87549.2k
1

That is fine. Thanks for modifying the format of the post.

ADD REPLYlink written 2.0 years ago by giuseppe052520
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