Question: tximport error with Salmon in DESeq2 pipeline
0
gravatar for seyfim
16 months ago by
seyfim0
seyfim0 wrote:

Hello,

I am following the Analyzing RNA-seq data with DESeq2 guide by Michael Love, Simon Anders and Wolfgang Huber 2018

here is my command that is throwing me an error:

txi<-tximport(filez, type=c("salmon"), tx2gene=tx2gene) 

Here is the error:

reading in files
1 Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  unused argument (col_names = c("Name", "Length", "TPM", "NumReads"))
Error in tximport(filez, type = c("salmon"), tx2gene = tx2gene) : 
  tried but couldn't use reader() without error
  user will need to define the importer() as well

I have tried calling the importer library:

source("https://bioconductor.org/biocLite.R")
biocLite("importer")

but it is not available for R 3.3.4 and I am not sure what to do...

 

deseq2 salmon tximport • 305 views
ADD COMMENTlink modified 16 months ago by Michael Love24k • written 16 months ago by seyfim0
Answer: tximport error with Salmon in DESeq2 pipeline
0
gravatar for Michael Love
16 months ago by
Michael Love24k
United States
Michael Love24k wrote:

Can you update the readr package? Also a good idea to always post your sessionInfo() when posting a question. I'm wondering if you have an old version that didn't include the col_names argument. Don't know when this was introduced to readr.

ADD COMMENTlink written 16 months ago by Michael Love24k
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