Error while using EdgeR

Question

[KVC_bioinfo]

Hello All,

I am trying to do differential expression using voom package. I constantly get the following error:

> Error in .isAllZero(counts) :    count matrix must be integer or
> double-precision

Below is the code I am trying:

library(limma)
library(preprocessCore)
library(edgeR)
library(tidyverse)

raw.data <- read.table(file="input.txt", header=TRUE)

tail(raw.data)
sample_info <- data.frame(condition = gsub( "_[0-93]+", "",names(raw.data)
),row.names = names(raw.data))
#sample_info

sample_info.edger <- factor(c( rep("sample", 84) , rep("Control", 8)))
sample_info.edger <- relevel( sample_info.edger , ref = "Control")

edgeR.DGElist <- DGEList(counts = raw.data , group = sample_info.edger )

Could someone help me here?

TIA

[h.mon]

Which step exactly causes the error? Is it edgeR.DGElist <- DGEList(counts = raw.data.m , group = sample_info.edger )?

What is the output of head(raw.data.m)?

[KVC_bioinfo]

edgeR.DGElist <- DGEList(counts = raw.data.m , group = sample_info.edger )

causes error.

raw.data.m was a typo sorry about that

[h.mon]

What is the output of head(raw.data.m)?

[theobroma22]

Do you have NAs or Infs in your matrix? How did you normalize your data?

[KVC_bioinfo]

I do not have NA. I used quantile normalization using Bioconductor.

Answer 1

[Gordon Smyth]

This is frequently asked question, see:

error while making a DegList object on R using edgeR package (Error in colSums(counts) : 'x' must be numeric)