I am looking to remove all samples that failed to sequence indicated by low lib.size from a DGEList using filterByExpr. I want to remove all samples that has lib.size less then 3000.000 (side question, why the 3 decimal places?)
I have manipulated the User Guide base code in a variety of intuitive ways without success.
y <- DGEList(counts=x,group=group) keep <- filterByExpr(y) y <- y[keep,,keep.lib.sizes=FALSE]
I wish I could post an image of my DEGList but images are not allowed. I'll just have to describe the DEGList. It contains counts double [48279 X 78] and then a subfolder of samples - list [78 X 3], groups - factor, lib.size - double, norm.factors - double.
I appreciate any suggestions you might have. Thank you.