Live and rendered notebooks

AlexsLemonade · Dec 6, 2024 · 6e25532 · 6e25532
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diff --git a/RNA-seq/02-gastric_cancer_tximeta.nb.html b/RNA-seq/02-gastric_cancer_tximeta.nb.html
@@ -3264,8 +3264,8 @@ <h2>Summarize to gene</h2>
 <pre class="r"><code># Summarize to the gene level
 gene_summarized &lt;- summarizeToGene(txi_data)</code></pre>
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-<pre><code>loading existing EnsDb created: 2024-12-04 21:59:44</code></pre>
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+<pre><code>loading existing EnsDb created: 2024-12-06 16:59:27</code></pre>
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 <pre><code>obtaining transcript-to-gene mapping from database</code></pre>

diff --git 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
diff --git a/scRNA-seq-advanced/03-differential_expression.nb.html b/scRNA-seq-advanced/03-differential_expression.nb.html