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develop/07_extra_contrast_design.html

@@ -469,19 +469,19 @@ <h2 class="anchored" data-anchor-id="one-factor-two-levels">One factor, two leve
 <pre><code>log2 fold change (MLE): condition_treat_vs_control effect 
 Wald test p-value: condition_treat_vs_control effect 
 DataFrame with 1000 rows and 6 columns
-           baseMean log2FoldChange     lfcSE      stat      pvalue        padj
-          &lt;numeric&gt;      &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;   &lt;numeric&gt;   &lt;numeric&gt;
-gene1       29.9039      -0.204440  0.674682 -0.303017  0.76187708   0.8511944
-gene2       21.6131       2.717021  0.911037  2.982340  0.00286054   0.0116004
-gene3       62.3118      -0.402178  0.492920 -0.815908  0.41455252   0.5479453
-gene4      263.7359       1.169000  0.479419  2.438365  0.01475386   0.0454685
-gene5       10.3583      -1.592500  1.351041 -1.178720  0.23850966   0.3848979
-...             ...            ...       ...       ...         ...         ...
-gene996  1349.32195       2.900516  0.432587  6.705042 2.01349e-11 3.83771e-10
-gene997     5.04273      -0.550290  1.451426 -0.379137 7.04586e-01 8.02235e-01
-gene998    27.38637       0.763575  0.659589  1.157654 2.47005e-01 3.91674e-01
-gene999    22.08201       0.899552  0.747721  1.203058 2.28954e-01 3.76746e-01
-gene1000   68.91083       0.458193  0.622865  0.735621 4.61962e-01 5.94932e-01</code></pre>
+          baseMean log2FoldChange     lfcSE      stat      pvalue        padj
+         &lt;numeric&gt;      &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;   &lt;numeric&gt;   &lt;numeric&gt;
+gene1      25.8214      -1.657436  0.746256 -2.221002 0.026350827  0.06788688
+gene2      25.6591      -1.545694  0.771022 -2.004735 0.044991347  0.10106431
+gene3     359.4599       0.304701  0.408977  0.745032 0.456252465  0.58632952
+gene4      10.7757      -4.525107  1.257925 -3.597279 0.000321563  0.00165687
+gene5      14.3918       0.905835  0.829287  1.092306 0.274698406  0.40864563
+...            ...            ...       ...       ...         ...         ...
+gene996    4.61750      -1.771386  1.342941 -1.319035 1.87158e-01 3.05892e-01
+gene997  121.62425      -4.059413  0.526814 -7.705591 1.30239e-14 4.94907e-13
+gene998   24.81257      -2.949839  0.720813 -4.092380 4.26969e-05 2.72305e-04
+gene999   23.15334       2.138521  0.710810  3.008571 2.62479e-03 1.00159e-02
+gene1000   9.74465       0.671829  0.977304  0.687431 4.91811e-01 6.18090e-01</code></pre>
 </div>
 </div>
 <p>The above is a simple way to obtain the results of interest. But it is worth understanding how DESeq is getting to these results by looking at the model’s matrix. DESeq defines the model matrix using base R functionality:</p>
@@ -854,15 +854,15 @@ <h2 class="anchored" data-anchor-id="extra-why-not-define-a-new-group-in-our-des
 <pre><code>DataFrame with 9 rows and 3 columns
         bloodtype sizeFactor      A_B
          &lt;factor&gt;  &lt;numeric&gt; &lt;factor&gt;
-sample1    bloodA   0.966444    TRUE 
-sample2    bloodA   0.974813    TRUE 
-sample3    bloodA   0.949976    TRUE 
-sample4    bloodB   0.927202    TRUE 
-sample5    bloodB   0.961256    TRUE 
-sample6    bloodB   1.199805    TRUE 
-sample7    bloodO   1.167588    FALSE
-sample8    bloodO   1.194509    FALSE
-sample9    bloodO   1.067843    FALSE</code></pre>
+sample1    bloodA   0.960307    TRUE 
+sample2    bloodA   0.921604    TRUE 
+sample3    bloodA   0.954911    TRUE 
+sample4    bloodB   0.903013    TRUE 
+sample5    bloodB   0.947941    TRUE 
+sample6    bloodB   1.154076    TRUE 
+sample7    bloodO   1.163800    FALSE
+sample8    bloodO   1.140992    FALSE
+sample9    bloodO   1.086946    FALSE</code></pre>
 </div>
 </div>
 <p>and then re-run DESeq with a new design:</p>

develop/09_summarized_workflow.html

@@ -29567,32 +29567,32 @@ <h3 class="anchored" data-anchor-id="perform-gsea-analysis-of-kegg-pathways-can-
 <div class="cell-output cell-output-stdout">
 <pre><code>               ID                                       Description setSize
 hsa05322 hsa05322                      Systemic lupus erythematosus     122
-hsa03040 hsa03040                                       Spliceosome     140
 hsa05010 hsa05010                                 Alzheimer disease     342
-hsa05014 hsa05014                     Amyotrophic lateral sclerosis     307
 hsa05022 hsa05022 Pathways of neurodegeneration - multiple diseases     420
+hsa05014 hsa05014                     Amyotrophic lateral sclerosis     307
 hsa05020 hsa05020                                     Prion disease     228
+hsa03040 hsa03040                                       Spliceosome     140
          enrichmentScore       NES       pvalue    p.adjust      qvalue rank
-hsa05322       0.6077929  1.910901 2.255686e-05 0.001969260 0.001622274 1353
-hsa03040      -0.5236675 -1.700643 2.854000e-05 0.001969260 0.001622274 3820
-hsa05010      -0.4377507 -1.587096 2.657064e-05 0.001969260 0.001622274 4330
-hsa05014      -0.4449457 -1.585470 1.890851e-05 0.001969260 0.001622274 4938
-hsa05022      -0.4260198 -1.571919 2.037957e-05 0.001969260 0.001622274 3743
-hsa05020      -0.4681608 -1.617159 1.250698e-04 0.007191515 0.005924361 4938
+hsa05322       0.6077929  1.896791 2.430619e-05 0.002795212 0.002277107 1353
+hsa05010      -0.4377507 -1.572878 1.928279e-05 0.002795212 0.002277107 4330
+hsa05022      -0.4260198 -1.558893 1.056975e-05 0.002795212 0.002277107 3743
+hsa05014      -0.4449457 -1.583545 3.615685e-05 0.003118529 0.002540495 4938
+hsa05020      -0.4681608 -1.610366 5.256934e-05 0.003627284 0.002954950 4938
+hsa03040      -0.5236675 -1.716528 1.146697e-04 0.005289313 0.004308914 3820
                            leading_edge
 hsa05322  tags=21%, list=7%, signal=20%
-hsa03040 tags=39%, list=19%, signal=32%
 hsa05010 tags=40%, list=21%, signal=32%
-hsa05014 tags=44%, list=24%, signal=34%
 hsa05022 tags=34%, list=18%, signal=28%
+hsa05014 tags=44%, list=24%, signal=34%
 hsa05020 tags=46%, list=24%, signal=35%
+hsa03040 tags=39%, list=19%, signal=32%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   core_enrichment
 hsa05322                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  3122/8370/554313/8367/3017/8360/940/8344/8329/128312/8349/8341/723790/8357/8343/718/942/8336/8358/92815/440689/8970/8347/3586/8353/8348
-hsa03040                                                                                                                                                                                                                                                                                                                                                                                      23451/4116/988/6632/10992/9128/7307/102724594/11017/6625/6636/9410/6429/9775/22985/124904135/124904136/124904137/124904138/124904139/124904140/124904141/124904142/124904143/124904144/124907963/124907964/124907965/9343/9785/51503/27316/1655/6635/4686/6637/11325/3178/84991/57819/4809/24148/84321/2521/151903/3312/9129/8683/220988/9939/6631/6634/10262/10594
 hsa05010                                  5718/10476/8883/5682/1337/5663/776/5683/10297/8660/4694/518/5481/513/207/4710/29985/5689/10376/1329/5706/1349/4716/842/369/292/8503/29982/3630/4696/1459/514/5684/4035/55334/1460/4713/516/4715/7419/515/5714/3799/8517/4728/126328/64837/91252/10313/805/9377/5293/317/4723/836/8326/9861/54361/8678/4718/8408/5691/4717/5687/4707/64116/1139/1131/5704/23516/324/3553/7477/5602/1855/5705/5702/8322/27035/4725/5707/5692/203068/2475/81027/8851/5701/4514/488/5708/26100/5609/5715/1857/23236/4702/3265/3569/808/5599/355/7124/3552/3845/4722/4891/4720/5709/10105/8312/55851/4726/7473/5532/1020/10000/4311/4893/22863/5664/572/9776/5295/2932/22943/11047/2776/50507/11211/4519/5970/4539/1536/81029/4541/4040/2902
-hsa05014                            51807/10718/1351/2891/1965/7186/2876/57122/23165/506/3800/51079/23064/9818/55967/1537/596/9688/5718/10476/1769/5682/642659/1337/23435/5683/55746/29979/8480/4694/518/513/201625/4710/9972/5689/100101267/10376/1329/6396/5706/129401/5603/1349/4716/842/29982/4696/283/514/5684/9217/4713/516/4715/10121/515/5714/10671/11258/3799/4728/126328/64837/5606/9377/317/4723/836/55860/9861/8678/4718/8408/4686/5691/5071/4717/6647/5687/55916/4707/79139/5704/5705/10762/5702/3178/79902/4725/81929/5707/5692/203068/2475/81027/5701/4514/5708/311/26100/5715/5903/4702/10482/2521/581/7124/4722/4720/5709/220988/10010/84516/4726/5532/9782/8878/22863/572/9776/7415/4747/11047/5608/60/2878/4519/4539/55567/25981/4541/598/2902
 hsa05022 5689/10376/1329/7327/5706/5603/1349/4716/842/5335/369/292/29982/4696/1459/514/5684/9217/1460/4713/516/51465/4715/10121/7419/515/5714/10671/11258/3799/4728/126328/64837/5606/9927/805/9377/317/4723/836/3064/7311/8326/55860/9861/54361/8678/4718/8408/5691/5071/4717/6647/5687/4707/1139/1131/79139/5704/10131/324/3553/7477/5602/1855/5705/5702/8322/27035/4725/5707/5692/11315/203068/2475/81027/8851/5701/4514/488/5708/26100/5609/5715/1857/578/23236/4702/5578/3265/3569/808/5599/355/2521/581/7124/3552/3845/7326/4722/4720/5709/120892/10105/10010/8312/84516/356/4726/818/7473/5532/1020/8878/4893/22863/5664/7332/572/9776/2932/22943/7345/7415/4747/11047/5608/2776/50507/11211/2878/4519/5970/4539/1536/55567/81029/25981/4541/4040/598/2902
-hsa05020                                                                                                                                                                                                            51807/5594/1351/10963/1965/5595/506/3800/51079/5621/55967/1537/5718/10476/5682/1337/776/5683/1388/4694/518/513/4710/5689/10376/1329/5706/5603/1349/4716/842/292/8503/4696/1459/514/5684/1460/4713/516/4715/7419/4851/515/5714/3799/4728/126328/64837/9377/5293/317/4723/836/9861/4718/5691/4717/1535/6647/857/5687/4707/5704/3553/5602/5705/5702/4725/5707/5692/203068/81027/5701/10488/4514/6352/5708/5715/4702/3569/5599/581/7124/3552/3312/4722/4720/5709/10105/4726/5532/5880/572/5566/1958/5295/2932/11047/4519/4539/1536/4541/4684/2902</code></pre>
+hsa05014                            51807/10718/1351/2891/1965/7186/2876/57122/23165/506/3800/51079/23064/9818/55967/1537/596/9688/5718/10476/1769/5682/642659/1337/23435/5683/55746/29979/8480/4694/518/513/201625/4710/9972/5689/100101267/10376/1329/6396/5706/129401/5603/1349/4716/842/29982/4696/283/514/5684/9217/4713/516/4715/10121/515/5714/10671/11258/3799/4728/126328/64837/5606/9377/317/4723/836/55860/9861/8678/4718/8408/4686/5691/5071/4717/6647/5687/55916/4707/79139/5704/5705/10762/5702/3178/79902/4725/81929/5707/5692/203068/2475/81027/5701/4514/5708/311/26100/5715/5903/4702/10482/2521/581/7124/4722/4720/5709/220988/10010/84516/4726/5532/9782/8878/22863/572/9776/7415/4747/11047/5608/60/2878/4519/4539/55567/25981/4541/598/2902
+hsa05020                                                                                                                                                                                                            51807/5594/1351/10963/1965/5595/506/3800/51079/5621/55967/1537/5718/10476/5682/1337/776/5683/1388/4694/518/513/4710/5689/10376/1329/5706/5603/1349/4716/842/292/8503/4696/1459/514/5684/1460/4713/516/4715/7419/4851/515/5714/3799/4728/126328/64837/9377/5293/317/4723/836/9861/4718/5691/4717/1535/6647/857/5687/4707/5704/3553/5602/5705/5702/4725/5707/5692/203068/81027/5701/10488/4514/6352/5708/5715/4702/3569/5599/581/7124/3552/3312/4722/4720/5709/10105/4726/5532/5880/572/5566/1958/5295/2932/11047/4519/4539/1536/4541/4684/2902
+hsa03040                                                                                                                                                                                                                                                                                                                                                                                      23451/4116/988/6632/10992/9128/7307/102724594/11017/6625/6636/9410/6429/9775/22985/124904135/124904136/124904137/124904138/124904139/124904140/124904141/124904142/124904143/124904144/124907963/124907964/124907965/9343/9785/51503/27316/1655/6635/4686/6637/11325/3178/84991/57819/4809/24148/84321/2521/151903/3312/9129/8683/220988/9939/6631/6634/10262/10594</code></pre>
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develop/index.html

@@ -383,7 +383,7 @@ <h4>Authors</h4>
 
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