I have RNA-Seq data from human tissues and I was wondering if I can add the batches in my additive model like this? (The batches are different dates of RNA extraction from tissue.)
x <- read.delim("rawCountMatrix.txt", row.names = "Gene") group <- factor(c(1,2,2,2,2,2,1,1,1,1)) RIN <- c(5.6,7.6,6.7,5.6,7.6,6.4,6.8,7.7,5.7,8.3) Age <- c(106,89,76,82,87,87,73,77,78,88) PMI <- c(20.58,15.16,20.17,19.16,21.66,22,22,13.5,12.83,14.5) Batch <- factor(c("a","a","b","a","a","c","a","c","a","c")) design <- model.matrix(~group + Age + RIN + PMI + Batch) y <- DGEList(counts=x,group=group) y <- calcNormFactors(y) design <- model.matrix(~group + RIN + Age + PMI) y <- estimateDisp(y,design) fit <- glmFit(y,design) lrt <- glmLRT(fit)
If yes, is it the best way to consider batch effects for a well designed study?
I appreciate any help or comments!