I am starting with RUVseq and I have questions and some errors to understand-solve.
First (sorry if it is really naive question) I would like to know if it is possible to introduce ERCC spikes a posteriori in our data. I guess the answer will be no, but maybe you have tried or you have some suggestions. We have mouse ran-seq.
I am using the other two alternatives with the next error messages:
> differences<- matrix(data=c(1:2, 3:4), byrow=TRUE, nrow=2)
[1,] 1 2
[2,] 3 4
Error in solve.default(a[, cIdx, drop = FALSE] %*% t(a[, cIdx, drop = FALSE]), :
no right-hand side in 'b'
I guess the problem is the number of replicates (only 2) , but I don't know how to set it up correctly.
For RUVr I think I have the same problem:
> set4<-RUVr(set, genes, k=1, res)
Error in svd(E[, cIdx]) : a dimension is zero
I have been trying to set "cIdx" by reading the reference manual, but I couldn't achieve it to work properly.
Thanks in advance. Best,