I have 3 pairs of samples (treatment + control) from 3 donors.
When perform PCA or MDS, I found samples were separated into 3 clusters, each corresponding to 1 donor. Consistently, number of DEGs were few between treatment and control.
Is it possible, or reasonable, to remove such donor effect before further analysis?
/* Here are some related codes:
donor = factor(coldata$Patient)
Treat = factor(coldata$Treatment, levels=c("Control","One_important_gene")))
design = model.matrix(~donor+Treat)
y = DGEList(counts=matrix_of_raw_read_count)
keep = rowSums(cpm(y) > 2.0) >= 3
y = y[keep,,keep.lib.sizes=FALSE]
y = calcNormFactors(y)
y = estimateDisp(y,design,robust=TRUE)
fit = glmFit(y,design,robust=TRUE)
lrt = glmLRT(fit,coef="One_important_gene")