Good morning,

I am analyzing RNAseq data from 2 different populations exposed to 2 experimental treatments. I get the following error when running edgeR: "error in dispCoxReid(y, design=design, offset=offset, subset=subset, : no data rows with required number of counts." After this error is reported, R freezes and I must force quit the program. Im not using this function in my code so I am unsure why I am getting the error message. Interestingly, I get the error when I run the code on a .csv file containing values I obtained by dividing raw counts by the sum of all counts in a library to correct for differences in size across libraries (i.e. proportional counts). When I run the code on a .csv file containing the raw counts, I do not get the error message. My code and the error message are below. Any advice is much appreciated.

library("edgeR")
x=read.csv("~/EGS/proportions.csv", header = TRUE)
rownames(x) <- x[,1]; 
x <- as.matrix(x[,-1]) 
keep <- rowSums(cpm(x)>1) >= 9 
z<- x[keep,] 
group <- factor(c(1,1,2,2,2,3,3,4,4)) 
population <- factor(c(1,1,2,2,2,1,1,2,2))
salinity <- factor(c(1,1,1,1,1,2,2,2,2))
design <- model.matrix(~population + salinity)
y <-DGEList(counts=z, group=group)
y <- calcNormFactors(y) 
y <- estimateGLMCommonDisp(y,design)

Error in dispCoxReid(y, design = design, offset = offset, subset = subset, : no data rows with required number of counts

You are trying to be tricky when that isn't necessary, nor helpful. edgeR expects the counts, and is quite capable of accounting for the library size without any pre-processing on your part. When you try to account for the library sizes you are actually undermining your analysis, as edgeR is expecting integer counts, and will not work correctly if you feed in something else.

In future, when you show your code, please try to cut down to just what is necessary to show your problem. Keeping in all that other stuff is not helpful.