Chao Gao

Hi, you might refer to #229 about finding the proper K. As for lambda, 5 would usually work. Hope this helps!

Hi @elhaam , LIGER for iNMF requires the genes to be the same for input datasets (genes by cells matrices). It is likely that the inputs were cells by genes...

Hi, If you'd like to split the plot by time (Assuming each input dataset corresponds to one time point), you could try the following customized code: ``` library(ggplot2) tsne_df

Hi Karl, Thank you for your valuable input. We have adopted your suggestion. If the `quantile_norm` with `dims.use` (Thanks @samuel-marsh for bringing it up) still does not resolve the issue...

Hi Nils, Very sorry about the late reply. We've incorporated your suggested fix on `subsetLiger` function. Thank you for identifying this issue and your effort to improve rliger! Best, Chao

Hi Sam, Are you operating on the same set of h5 files (11 in total) with different filters? When you call the `normalize()`, there will be a slot called cell.data...

Hello Sam, Once a Seurat object is converted to a Liger object through `seuratToLiger()`, the cell.data is generated in the liger object. Hence it is necessary to re-convert if different...

Hi Sam, Thanks for the reminder! It is in our plan. Best, Chao

Hi Sam and Jonah, Sorry for the inconvenience brought by renaming the package and thanks for bringing it to discussion. As of right now, it seems there is no other...

Hi @mtegtmey , Sorry about the late reply. Have you resolved this issue yet? If not, do you mind sharing a code snippet where you ran into this issue? Best,