log-transform data

[krishnaswamylab]

log-transform data

[dvdijk]

It doesn't have to be, but it can.
Either: raw count matrix -> library size normalize -> MAGIC
or: raw count matrix -> library size normalize -> log transform (don't forget pseudo count) -> MAGIC

[yanwu2014]

Thanks! Btw there seems to be a bug in the current log_transform function (should it be referencing self.data instead of scdata.data?)

Also this method is awesome! It runs super fast and seems to work well on our datasets so far!