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diff --git a/heartMainInteraction.html b/heartMainInteraction.html
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diff --git a/index.html b/index.html
@@ -440,10 +440,10 @@ <h4>2.2. Preprocessing &amp; Analysis of Label Free Quantitative
 <li>Wrap-up Peptide-based Models: <a
 href="./pda_robustSummarisation_peptideModels.html">html</a>, <a
 href="./pda_robustSummarisation_peptideModels.pdf">pdf</a></li>
-<li>Solutions: <a href="cancer3x3.html">cancer3x3</a>, <a
-href="cancer6x6.html">cancer6x6</a>, <a
-href="cancer9x9.html">cancer9x9</a></li>
 </ul>
+<!--
+  - Solutions: [cancer3x3](cancer3x3.html), [cancer6x6](cancer6x6.html), [cancer9x9](cancer9x9.html)
+-->
 </div>
 <div
 id="statistical-inference-analysis-of-experiments-with-factorial-designs"

diff --git a/multipleRegression_KPNA2.html b/multipleRegression_KPNA2.html
@@ -819,8 +819,8 @@ <h1><span class="header-section-number">4</span> Assessing the
 grade3 == 0                  1.6675     0.1827   9.127  &lt; 0.001 ***
 grade3 + grade3:node1 == 0   0.8928     0.1827   4.886  &lt; 0.001 ***
 node1 == 0                   0.6577     0.1827   3.600  0.00718 ** 
-node1 + grade3:node1 == 0   -0.1170     0.1827  -0.640  0.89818    
-grade3:node1 == 0           -0.7748     0.2584  -2.998  0.02669 *  
+node1 + grade3:node1 == 0   -0.1170     0.1827  -0.640  0.89817    
+grade3:node1 == 0           -0.7748     0.2584  -2.998  0.02664 *  
 ---
 Signif. codes:  0 &#39;***&#39; 0.001 &#39;**&#39; 0.01 &#39;*&#39; 0.05 &#39;.&#39; 0.1 &#39; &#39; 1
 (Adjusted p values reported -- single-step method)</code></pre>
@@ -830,31 +830,31 @@ <h1><span class="header-section-number">4</span> Assessing the
 
 Fit: lm(formula = gene %&gt;% log2 ~ grade * node, data = kpna2)
 
-Quantile = 2.6995
+Quantile = 2.7009
 95% family-wise confidence level
 
 
 Linear Hypotheses:
                            Estimate lwr      upr     
-grade3 == 0                 1.66754  1.17431  2.16076
-grade3 + grade3:node1 == 0  0.89279  0.39956  1.38601
-node1 == 0                  0.65773  0.16450  1.15096
-node1 + grade3:node1 == 0  -0.11702 -0.61025  0.37621
-grade3:node1 == 0          -0.77475 -1.47228 -0.07722</code></pre>
+grade3 == 0                 1.66754  1.17405  2.16103
+grade3 + grade3:node1 == 0  0.89279  0.39930  1.38628
+node1 == 0                  0.65773  0.16424  1.15122
+node1 + grade3:node1 == 0  -0.11702 -0.61051  0.37647
+grade3:node1 == 0          -0.77475 -1.47265 -0.07685</code></pre>
 <div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="dv">2</span><span class="sc">^</span><span class="fu">confint</span>(fitGlht)<span class="sc">$</span>confint</span></code></pre></div>
 <pre><code>                       Estimate       lwr       upr
-grade3                3.1767209 2.2574278 4.4703781
-grade3 + grade3:node1 1.8567602 1.3194430 2.6128893
-node1                 1.5775997 1.1210672 2.2200462
-node1 + grade3:node1  0.9220906 0.6552521 1.2975939
-grade3:node1          0.5844896 0.3605427 0.9475384
+grade3                3.1767209 2.2571045 4.4710184
+grade3 + grade3:node1 1.8567602 1.3192540 2.6132636
+node1                 1.5775997 1.1209066 2.2203642
+node1 + grade3:node1  0.9220906 0.6551582 1.2977797
+grade3:node1          0.5844896 0.3604697 0.9477304
 attr(,&quot;conf.level&quot;)
 [1] 0.95
 attr(,&quot;calpha&quot;)
-[1] 2.69746</code></pre>
+[1] 2.69859</code></pre>
 <div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="dv">2</span><span class="sc">^-</span><span class="fu">confint</span>(fitGlht)<span class="sc">$</span>confint[<span class="st">&quot;grade3:node1&quot;</span>,]</span></code></pre></div>
 <pre><code>Estimate      lwr      upr 
-1.710895 2.773168 1.055529 </code></pre>
+1.710895 2.773489 1.055407 </code></pre>
 </div>
 <div id="conclusion" class="section level1" number="5">
 <h1><span class="header-section-number">5</span> Conclusion</h1>
@@ -870,7 +870,7 @@ <h1><span class="header-section-number">5</span> Conclusion</h1>
 tumors (95% CI [1.32, 2.61]).</p></li>
 <li><p>The association between the KPNA2 expression with the lymph node
 status in grade 1 patients is very significant (<span
-class="math inline">\(p=\)</span> 0.0073).<br />
+class="math inline">\(p=\)</span> 0.007).<br />
 The KPNA2 expression in histological grade 1 patients with affected
 lymph nodes is on average 1.58 times higher than for grade 1 patients
 with unaffected lymph nodes (95% CI [1.12, 2.22]). In grade 3 patients,

diff --git a/multipleRegression_KPNA2.pdf b/multipleRegression_KPNA2.pdf
diff --git a/multipleRegression_KPNA2_files/figure-html/unnamed-chunk-3-1.png b/multipleRegression_KPNA2_files/figure-html/unnamed-chunk-3-1.png
diff --git a/parathyroid.html b/parathyroid.html
@@ -527,7 +527,7 @@ <h4 class="date">statOmics, Ghent University (<a
 <pre><code>## Installation paths not writeable, unable to update packages
 ##   path: /opt/R/4.2.3/lib/R/library
 ##   packages:
-##     class, KernSmooth, lattice, spatial</code></pre>
+##     class, KernSmooth, lattice, rpart, spatial</code></pre>
 <pre><code>## Old packages: &#39;askpass&#39;, &#39;BH&#39;, &#39;BiocManager&#39;, &#39;BiocParallel&#39;, &#39;Biostrings&#39;,
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diff --git a/parathyroid.pdf b/parathyroid.pdf
diff --git a/parathyroid_files/figure-html/unnamed-chunk-13-2.png b/parathyroid_files/figure-html/unnamed-chunk-13-2.png
diff --git a/pda_blocking_wrapup.pdf b/pda_blocking_wrapup.pdf
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diff --git a/pda_quantification_inference.pdf b/pda_quantification_inference.pdf
diff --git a/pda_quantification_preprocessing.pdf b/pda_quantification_preprocessing.pdf
diff --git a/pda_robustSummarisation_peptideModels.pdf b/pda_robustSummarisation_peptideModels.pdf
diff --git a/recapGeneralLinearModel.html b/recapGeneralLinearModel.html
diff --git a/recapGeneralLinearModel.pdf b/recapGeneralLinearModel.pdf
diff --git a/recapGeneralLinearModel_files/figure-html/unnamed-chunk-4-1.png b/recapGeneralLinearModel_files/figure-html/unnamed-chunk-4-1.png
diff --git a/recapGeneralLinearModel_files/figure-html/unnamed-chunk-5-1.png b/recapGeneralLinearModel_files/figure-html/unnamed-chunk-5-1.png
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diff --git a/sequencing_countData.html b/sequencing_countData.html
@@ -511,7 +511,7 @@
 <h1 class="title toc-ignore">Introduction to Sequencing: Working with
 RNA-seq count data</h1>
 <h4 class="author">Koen Van den Berge &amp; Lieven Clement</h4>
-<h4 class="date">Last edited on 09 October, 2023</h4>
+<h4 class="date">Last edited on 10 October, 2023</h4>
 
 </div>
 

diff --git a/sequencing_countData.log b/sequencing_countData.log
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diff --git a/sequencing_countData.pdf b/sequencing_countData.pdf
diff --git a/sequencing_intro.html b/sequencing_intro.html
@@ -511,7 +511,7 @@
 <h1 class="title toc-ignore">Introduction to RNA-seq sequencing:
 Preprocessing</h1>
 <h4 class="author">Koen Van den Berge &amp; Lieven Clement</h4>
-<h4 class="date">Last edited on 09 October, 2023</h4>
+<h4 class="date">Last edited on 10 October, 2023</h4>
 
 </div>
 

diff --git a/sequencing_intro.log b/sequencing_intro.log
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diff --git a/sequencing_intro.pdf b/sequencing_intro.pdf
diff --git a/sequencing_singleCell.html b/sequencing_singleCell.html
@@ -510,7 +510,7 @@
 
 <h1 class="title toc-ignore">Sequencing: Single Cell RNA-seq</h1>
 <h4 class="author">Lieven Clement and Koen Van den Berge</h4>
-<h4 class="date">Last edited on 09 October, 2023</h4>
+<h4 class="date">Last edited on 10 October, 2023</h4>
 
 </div>
 
@@ -636,7 +636,7 @@ <h2><span class="header-section-number">1.5</span> Multiplexing</h2>
 <pre><code>## Installation paths not writeable, unable to update packages
 ##   path: /opt/R/4.2.3/lib/R/library
 ##   packages:
-##     class, KernSmooth, lattice, spatial</code></pre>
+##     class, KernSmooth, lattice, rpart, spatial</code></pre>
 <pre><code>## Old packages: &#39;askpass&#39;, &#39;BH&#39;, &#39;BiocManager&#39;, &#39;BiocParallel&#39;, &#39;Biostrings&#39;,
 ##   &#39;bit&#39;, &#39;blob&#39;, &#39;bookdown&#39;, &#39;boot&#39;, &#39;broom&#39;, &#39;bslib&#39;, &#39;cachem&#39;, &#39;callr&#39;,
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@@ -864,12 +864,12 @@ <h3><span class="header-section-number">2.2.2</span> Explore
 <pre><code>## DataFrame with 6 rows and 2 columns
 ##                                    Sample            Barcode
 ##                               &lt;character&gt;        &lt;character&gt;
-## AAACCTGAGAAACCAT-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAACCAT-1
-## AAACCTGAGAAACCGC-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAACCGC-1
-## AAACCTGAGAAACCTA-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAACCTA-1
-## AAACCTGAGAAACGAG-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAACGAG-1
-## AAACCTGAGAAACGCC-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAACGCC-1
-## AAACCTGAGAAAGTGG-1 /tmp/Rtmp16MrqY/pbmc.. AAACCTGAGAAAGTGG-1</code></pre>
+## AAACCTGAGAAACCAT-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAACCAT-1
+## AAACCTGAGAAACCGC-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAACCGC-1
+## AAACCTGAGAAACCTA-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAACCTA-1
+## AAACCTGAGAAACGAG-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAACGAG-1
+## AAACCTGAGAAACGCC-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAACGCC-1
+## AAACCTGAGAAAGTGG-1 /tmp/RtmpB9bIlJ/pbmc.. AAACCTGAGAAAGTGG-1</code></pre>
 <p><br/><br/></p>
 </div>
 <div id="use-sensible-gene-names" class="section level3" number="2.2.3">
@@ -1816,7 +1816,7 @@ <h4><span class="header-section-number">2.9.6.1</span> Example</h4>
 <pre><code>## Installation paths not writeable, unable to update packages
 ##   path: /opt/R/4.2.3/lib/R/library
 ##   packages:
-##     class, KernSmooth, lattice, spatial</code></pre>
+##     class, KernSmooth, lattice, rpart, spatial</code></pre>
 <pre><code>## Old packages: &#39;askpass&#39;, &#39;BH&#39;, &#39;BiocManager&#39;, &#39;BiocParallel&#39;, &#39;Biostrings&#39;,
 ##   &#39;bit&#39;, &#39;blob&#39;, &#39;bookdown&#39;, &#39;boot&#39;, &#39;broom&#39;, &#39;bslib&#39;, &#39;cachem&#39;, &#39;callr&#39;,
 ##   &#39;car&#39;, &#39;cli&#39;, &#39;clue&#39;, &#39;cluster&#39;, &#39;codetools&#39;, &#39;colorspace&#39;, &#39;commonmark&#39;,

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