day 4 material

ocbe-uio · Jan 17, 2024 · ae75506 · ae75506
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diff --git a/dev/lablecture_day4_clustering.key b/dev/lablecture_day4_clustering.key
diff --git a/docs/index.html b/docs/index.html
@@ -314,7 +314,7 @@ <h3 class="anchored" data-anchor-id="day-4">Day 4</h3>
 <tr class="odd">
 <td style="text-align: center;">13:00 - 14:00</td>
 <td style="text-align: center;">Take-home exam simulation</td>
-<td style="text-align: center;"></td>
+<td style="text-align: center;"><a href="">Exam</a></td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">14:00 - 16:00</td>

diff --git a/docs/lab/lab_day3_pca.html b/docs/lab/lab_day3_pca.html
@@ -192,7 +192,7 @@ <h2 id="toc-title">On this page</h2>
 
 <p>Download datasets <a href="https://github.com/ocbe-uio/course_med3007/tree/main/lab/data">here</a> or from Canvas.</p>
 <p>R script: <a href="https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab2_pca.R">Code</a></p>
-<p>Lab Lecture</p>
+<p>Lab Lecture: <a href="presentation/Lab_pca.pdf">Slides</a></p>
 <section id="exercise-1-food" class="level2">
 <h2 class="anchored" data-anchor-id="exercise-1-food">Exercise 1: Food</h2>
 <p>In the first exercise, we explore a low-dimensional dataset, <code>Food.txt</code>.</p>
@@ -985,7 +985,7 @@ <h2 class="anchored" data-anchor-id="exercise-3-gene-expression-data">Exercise 3
 <span id="cb69-11"><a href="#cb69-11" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb69-12"><a href="#cb69-12" aria-hidden="true" tabindex="-1"></a>R script: <span class="co">[</span><span class="ot">Code</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab2_pca.R)</span></span>
 <span id="cb69-13"><a href="#cb69-13" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb69-14"><a href="#cb69-14" aria-hidden="true" tabindex="-1"></a>Lab Lecture </span>
+<span id="cb69-14"><a href="#cb69-14" aria-hidden="true" tabindex="-1"></a>Lab Lecture: <span class="co">[</span><span class="ot">Slides</span><span class="co">](presentation/Lab_pca.pdf)</span></span>
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diff --git a/docs/lab/lab_day4_clustering.html b/docs/lab/lab_day4_clustering.html
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-complete-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-complete-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-cor-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-cor-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap1-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap1-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap2-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap2-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap3-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-heatmap3-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-linkage-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-linkage-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-linkage-2.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-linkage-2.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/hc-food-unscaled-1.png b/docs/lab/lab_day4_clustering_files/figure-html/hc-food-unscaled-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-keeppc-1.png b/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-keeppc-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-plot2-1.png b/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-plot2-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-plotpc-1.png b/docs/lab/lab_day4_clustering_files/figure-html/pca-nci-plotpc-1.png
diff --git a/...iles/figure-html/clust-nci60-cutree-1.png → ..._files/figure-html/unnamed-chunk-18-1.png b/...iles/figure-html/clust-nci60-cutree-1.png → ..._files/figure-html/unnamed-chunk-18-1.png
diff --git a/..._files/figure-html/unnamed-chunk-14-1.png → ..._files/figure-html/unnamed-chunk-25-1.png b/..._files/figure-html/unnamed-chunk-14-1.png → ..._files/figure-html/unnamed-chunk-25-1.png
diff --git a/docs/lab/lab_day4_clustering_files/figure-html/unnamed-chunk-7-1.png b/docs/lab/lab_day4_clustering_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/lab/overview.html b/docs/lab/overview.html
@@ -245,7 +245,7 @@ <h2 class="anchored" data-anchor-id="lab-notes-and-r-scripts">Lab notes and R sc
 <td style="text-align: center;">Day 4</td>
 <td style="text-align: center;"><a href="../lab/lab_day4_clustering.html">Day 4: Clustering</a></td>
 <td style="text-align: center;"><a href="https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab3_clustering.R">Code</a></td>
-<td style="text-align: center;"></td>
+<td style="text-align: center;"><a href="presentation/Lab_clustering.pdf">Slides</a></td>
 </tr>
 </tbody>
 </table>
@@ -579,7 +579,7 @@ <h2 class="anchored" data-anchor-id="lab-notes-and-r-scripts">Lab notes and R sc
 <span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a>| Day 2  | <span class="co">[</span><span class="ot">Day 2: Multiple testing</span><span class="co">](lab_day2_testing.qmd)</span>  |   <span class="co">[</span><span class="ot">Code</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab1.R)</span>, <span class="co">[</span><span class="ot">Code (solution)</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab1_exercise_solution.R)</span> | |</span>
 <span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a>| Day 3  | <span class="co">[</span><span class="ot">Day 3: Principal Component Analysis</span><span class="co">](lab_day3_pca.qmd)</span> |<span class="co">[</span><span class="ot">Code</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab2_pca.R)</span> | <span class="co">[</span><span class="ot">Slides</span><span class="co">](presentation/Lab_pca.pdf)</span></span>
 <span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a> |</span>
-<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a>| Day 4  | <span class="co">[</span><span class="ot">Day 4: Clustering</span><span class="co">](lab_day4_clustering.qmd)</span> |<span class="co">[</span><span class="ot">Code</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab3_clustering.R)</span> | |</span>
+<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a>| Day 4  | <span class="co">[</span><span class="ot">Day 4: Clustering</span><span class="co">](lab_day4_clustering.qmd)</span> |<span class="co">[</span><span class="ot">Code</span><span class="co">](https://github.com/ocbe-uio/course_med3007/blob/main/lab/code/MED3007_Lab3_clustering.R)</span> | <span class="co">[</span><span class="ot">Slides</span><span class="co">](presentation/Lab_clustering.pdf)</span>|</span>
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 <span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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diff --git a/docs/lab/presentation/Lab_clustering.pdf b/docs/lab/presentation/Lab_clustering.pdf