diff --git a/NEWS.md b/NEWS.md index 47425ac..60af7ca 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,8 @@ - Ability to do downstream analysis on H5 data - Pseudo-bulk should be easy because we are just aggregating cells. - Wilcoxon might be a bit harder because ranks are calculated per gene but the H5 sparse data is column majored. Might need to find a fast on-disk transposition method. +- Fix runUINMF aborting criteria + - UINMF is capable of running with k > number of shared genes. Don't have to abort on it. ## rliger 2.0.0 diff --git a/vignettes/articles/STARmap_dropviz_vig.Rmd b/vignettes/articles/STARmap_dropviz_vig.Rmd index 921123f..d19ca63 100644 --- a/vignettes/articles/STARmap_dropviz_vig.Rmd +++ b/vignettes/articles/STARmap_dropviz_vig.Rmd @@ -66,10 +66,8 @@ Unshared Integrative Non-negative Matrix Factorization (UINMF) can be applied wi In this tutorial, we set dataset specific lambda (regularization parameter) values to penalize the dataset specific effect differently. -Another noteworthy advantage of UINMF is that we are able to use a larger number of factors than there are shared features. We captilize on this by changing the default value of `k` to 40. - ```{r factorization} -lig <- runUINMF(lig, k = 40, lambda = c(10, 1)) +lig <- runUINMF(lig, k = 25, lambda = c(10, 1)) ``` ## Step 4: Quantile Normalization and Joint Clustering