Question: Error while using EdgeR
0
gravatar for KVC_bioinfo
23 months ago by
KVC_bioinfo410
Boston
KVC_bioinfo410 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 • 1.1k views
ADD COMMENTlink modified 11 months ago by Gordon Smyth1.4k • written 23 months ago by KVC_bioinfo410

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 23 months ago • written 23 months ago by h.mon29k
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 23 months ago by KVC_bioinfo410

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

ADD REPLYlink written 23 months ago by h.mon29k

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

ADD REPLYlink written 23 months ago by theobroma221.1k

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

ADD REPLYlink written 23 months ago by KVC_bioinfo410
0
gravatar for Gordon Smyth
11 months ago by
Gordon Smyth1.4k
Australia
Gordon Smyth1.4k 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 11 months ago • written 11 months ago by Gordon Smyth1.4k
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