Question: adding batch effects as a covariate in additive model in edgeR
gravatar for Victoria
3 months ago by
Victoria0 wrote:

Hello everyone,

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!

edger batch effects • 83 views
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