Question: Error while using EdgeR
0
gravatar for KVC_bioinfo
2.5 years ago by
KVC_bioinfo510
Boston
KVC_bioinfo510 wrote:

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

edger • 1.3k views
ADD COMMENTlink modified 18 months ago by Gordon Smyth1.9k • written 2.5 years ago by KVC_bioinfo510

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)?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by h.mon31k
edgeR.DGElist <- DGEList(counts = raw.data.m , group = sample_info.edger )

causes error.

raw.data.m was a typo sorry about that

ADD REPLYlink written 2.5 years ago by KVC_bioinfo510

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

ADD REPLYlink written 2.5 years ago by h.mon31k

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

ADD REPLYlink written 2.5 years ago by theobroma221.1k

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

ADD REPLYlink written 2.5 years ago by KVC_bioinfo510
0
gravatar for Gordon Smyth
18 months ago by
Gordon Smyth1.9k
Australia
Gordon Smyth1.9k wrote:

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)

ADD COMMENTlink modified 18 months ago • written 18 months ago by Gordon Smyth1.9k
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