Input and Output

[Winnie09]

Dear author,

Thanks for developing the software! I have a few questions but did not find clear answer from your paper:

1. is the input a count matrix?
2. is the output a count matrix? Has it been normalized by library size, or log2-transformed?
3. I tried to use a raw count matrix as an input, but find in output values are as large as 400+ and three quantiles are between 0 and 1?

Thanks!