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