From 6e25532626e749cf6e2360b9072fa151bc390422 Mon Sep 17 00:00:00 2001 From: sjspielman <4701111+sjspielman@users.noreply.github.com> Date: Fri, 6 Dec 2024 17:16:15 +0000 Subject: [PATCH] Live and rendered notebooks --- RNA-seq/02-gastric_cancer_tximeta.nb.html | 4 +-- .../02-dataset_integration-live.Rmd | 8 ++--- .../02-dataset_integration.nb.html | 34 +++++-------------- .../03-differential_expression.nb.html | 2 +- 4 files changed, 14 insertions(+), 34 deletions(-) diff --git a/RNA-seq/02-gastric_cancer_tximeta.nb.html b/RNA-seq/02-gastric_cancer_tximeta.nb.html index 778bfb98..36238c1a 100644 --- a/RNA-seq/02-gastric_cancer_tximeta.nb.html +++ b/RNA-seq/02-gastric_cancer_tximeta.nb.html @@ -3264,8 +3264,8 @@

Summarize to gene

# Summarize to the gene level
 gene_summarized <- summarizeToGene(txi_data)
- -
loading existing EnsDb created: 2024-12-04 21:59:44
+ +
loading existing EnsDb created: 2024-12-06 16:59:27
obtaining transcript-to-gene mapping from database
diff --git a/scRNA-seq-advanced/02-dataset_integration-live.Rmd b/scRNA-seq-advanced/02-dataset_integration-live.Rmd index 107bc35c..ca0a06f2 100644 --- a/scRNA-seq-advanced/02-dataset_integration-live.Rmd +++ b/scRNA-seq-advanced/02-dataset_integration-live.Rmd @@ -702,9 +702,8 @@ Like `fastMNN`, `harmony` performs integration on a merged PCA matrix. However, unlike `fastMNN`, `harmony` does not "back-calculate" corrected expression from the corrected PCA matrix and it only returns the corrected PCA matrix itself. For input, `harmony` needs a couple pieces of information: -- First, `harmony` can either take a matrix of normalized expression values, from which it will calculate a batch-weighted PCA matrix to integrate, or it can take a batch-weighted PCA matrix directly to perform integration. -Since we already calculated a batch-weighted PCA matrix (our `merged_PCA` reduced dimension), we'll provide this information directly. - - We will need to specify the additional argument `do_pca=FALSE` to tell `harmony` that the input matrix we provided already is a PCA matrix. +- 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 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. @@ -715,8 +714,7 @@ To do this, we provide two arguments: Let's go! ```{r run harmony, live = TRUE} -# integrate with harmony, setting the argument `do_pca = FALSE` -# since we are providing a PCA matrix directly +# Run harmony integration ``` diff --git a/scRNA-seq-advanced/02-dataset_integration.nb.html b/scRNA-seq-advanced/02-dataset_integration.nb.html index ff74f293..5a02c685 100644 --- a/scRNA-seq-advanced/02-dataset_integration.nb.html +++ b/scRNA-seq-advanced/02-dataset_integration.nb.html @@ -4557,17 +4557,10 @@

Integration with harmony

itself. For input, harmony needs a couple pieces of information: