From da72b1a50494e8a2cc6d9c805b79d30d9e3ed64b Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 6 Dec 2024 11:32:24 -0500 Subject: [PATCH] Update 02-dataset_integration.Rmd Co-authored-by: Joshua Shapiro --- scRNA-seq-advanced/02-dataset_integration.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scRNA-seq-advanced/02-dataset_integration.Rmd b/scRNA-seq-advanced/02-dataset_integration.Rmd index 90d51e50..082a4912 100644 --- a/scRNA-seq-advanced/02-dataset_integration.Rmd +++ b/scRNA-seq-advanced/02-dataset_integration.Rmd @@ -740,7 +740,7 @@ However, unlike `fastMNN`, `harmony` does not "back-calculate" corrected express For input, `harmony` needs a couple pieces of information: - First, `harmony` takes a batch-weighted PCA matrix to perform integration. -We already calculated a batch-weighted PCA matrix (our `merged_PCA` reduced dimension), we'll provide this variable. +We already calculated a batch-weighted PCA matrix (our `merged_PCA` reduced dimension), we'll provide this as the the input. - Second, we need to tell `harmony` about the covariates to use - `sample` and `patient`. To do this, we provide two arguments: - `meta_data`, a data frame that contains covariates across samples.