Error when trying to run normOffsets
sjquon opened this issue · comments
csaw version 1.16.0
I am trying to run csaw, and when I get to the step to eliminate efficiency bias, I am encountering an error as seen below.
My command:
filtered.me<-normOffsets(filtered.me, se.out=T)
Error Message:
Error in calcNormFactors.default(assay(object, i = assay.id, withDimnames = FALSE), : formal argument "lib.size" matched by multiple actual arguments
3. calcNormFactors(assay(object, i = assay.id, withDimnames = FALSE), lib.size = lib.sizes, doWeighting = weighted, ...)
2. normFactors(object, lib.size = lib.sizes, ..., assay.id = assay.id, se.out = se.out)
1. normOffsets(filtered.me, se.out = T, param = param)
I can't figure out why I am getting this error code and how to fix it. I've tried searching the error message but haven't come up with anything. I would be very grateful if you have any ideas on how I can solve this.
I have attached a copy of my RMD file.
RStudio.pdf
Just call normFactors() directly, the use of type="scaling" is deprecated (see the warning).
Note that your error message says you are calling normOffsets(filtered.me, se.out = T, param = param). The param= should not be a legal argument to this function.