edgeR: DGElist error reported ' NA counts not allowed'.

Question

[amysays]

I had a problem when I run edge package in R, y <- DGEList(counts=data,group=group) reproted Error: NA counts not allowed, Please help

library(edgeR)

data <- read.csv("C:/Users/Amy/Desktop/11.csv",head=T,row.names = 1,sep=",",na.strings = "null")

head(data,n=5)

GSM545762 GSM545763 GSM545754 GSM545750 GSM545765 GSM545744 GSM545766
S100B  0.753269        NA        NA   2.95108    7.3952   1.17652   1.66002
BDNF  71.577800  25.49750  44.79810  19.42290   10.0199  14.69200  32.65380
TNF   38.054500  25.71950  20.99770  21.94090   36.0724  26.61190  26.89650
IL4   13.625200  10.29350   9.81751  13.17780   18.2236   2.90933  18.12220
IL2   12.646900   7.21491   7.44935  11.99540   11.1445   4.07951   3.67883

dim(data)

[1] 10 42

group <- factor(c(rep("Patients",23),rep("Controls",19))) group

[1] Patients Patients Patients Patients Patients Patients Patients Patients Patients
[10] Patients Patients Patients Patients Patients Patients Patients Patients Patients
[19] Patients Patients Patients Patients Patients Controls Controls Controls Controls
[28] Controls Controls Controls Controls Controls Controls Controls Controls Controls
[37] Controls Controls Controls Controls Controls Controls
Levels: Controls Patients

y <- DGEList(counts=data,group=group)

Error: NA counts not allowed

Answer 1

[ATpoint]

These are array data, edgeR is for RNA-seq, just saying... For this error, well the error is clear, NAs are not allowed and your data have NAs. If this was RNA-seq this would not even be possible since counts cannot be absent but only zero. Check the limma package for microarray analysis.

[amysays]

Yeah，Thanks for your reply，But I don't how to cancel the NA

[Kevin Blighe]

First try to determine why the NAs are in your data. It would be mal-practice to simply replace them with a value without understanding why they exist in the first place.

Also, as ATpoint says, these are microarray samples, so, you should be using Limma.