Thank you for such an amazing and useful tool.
I am currently applying URD on constructing developmental trees of our own datasets. As we had sequenced two batches of the end stage samples, we wanted to correct batch effect in defining those tip cells.
Your SupplementaryAnalysis.pdf tutorial is very useful, yet I found there might be two typos:
On page 19 --- Batch correct data, the pipeline used mnnCorrect method, and on page 18, library(scran) was noted as Batch correction using MNN. I wonder if this is a typo, and is this mnnCorrect function imported from the batchelor package?
On page 19 --- logupx.6s.mnn <- do.call("cbind", logupx.6s.mnn[[1]]) this command reported an error since do.call function needs the 2nd argument must be a list.
Thank you for such an amazing and useful tool. I am currently applying URD on constructing developmental trees of our own datasets. As we had sequenced two batches of the end stage samples, we wanted to correct batch effect in defining those tip cells. Your SupplementaryAnalysis.pdf tutorial is very useful, yet I found there might be two typos:
logupx.6s.mnn <- do.call("cbind", logupx.6s.mnn[[1]])this command reported an error since do.call function needs the 2nd argument must be a list.I am looking forward to your reply.