text: user2005: I compared two manually defined clusters using Seurat package function FindAllMarkers and got the output:
  
  Now, I am confused about three things:
  
  What are pct.1 and pct.2?
  How come p-adjusted values equal to 1? What does it mean?
  If we take first row, what does avg_logFC value of -1.35264 mean when we have cluster 0 in the cluster column? Is it that in cluster 0 the Cttnbp2 gene downregulated by a factor of 2^1.35264?
  
  
  user181: 
  pct.1– The percentage of cells where the gene is detected in the first group
  
  p_val_adj– Adjusted p-value, based on bonferroni correction using all genes in the dataset.
  
  
  
  This is not also known as a false discovery rate (FDR) adjusted p-value.
  
  An adjusted p-value of 1.00 means that after correcting for multiple testing, there is a 100% chance that the result (the logFC here) is due to chance.
  
  You are correct. The expression of Cttnbp2 donwn-regulated by that factor. If you were to look in the table at the cluster 1 DE genes you would see Cttnbp2 with a logFC value of 1.35264. When you are looking at genes differentailly expressed in only two clusters, the sign is the only thing that changes.
  
  Vignette posted above by @heathobrien.
  
original_text: 2005: <p>I compared two manually defined clusters using <code>Seurat</code> package function <code>FindAllMarkers</code> and got the output:</p>
  
  <p><a href="https://i.stack.imgur.com/yja4Q.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/yja4Q.png" alt="enter image description here"></a></p>
  
  <p>Now, I am confused about three things:</p>
  
  <ol>
  <li>What are <code>pct.1</code> and <code>pct.2</code>?</li>
  <li>How come <code>p-adjusted values</code> equal to <code>1</code>? What does it mean?</li>
  <li>If we take first row, what does <code>avg_logFC</code> value of <code>-1.35264</code> mean when we have cluster <code>0</code> in the <code>cluster</code> column? Is it that in cluster <code>0</code> the <code>Cttnbp2</code> gene downregulated by a factor of <code>2^1.35264</code>?</li>
  </ol>
   181: <ol>
  <li><p><code>pct.1</code>– The percentage of cells where the gene is detected in the first group</p>
  </li>
  <li><p><code>p_val_adj</code>– Adjusted p-value, based on bonferroni correction using all genes in the dataset.</p>
  </li>
  </ol>
  <blockquote>
  <p>This is <strong>not</strong> also known as a false discovery rate (FDR) adjusted p-value.</p>
  </blockquote>
  <p>An adjusted p-value of 1.00 means that after correcting for multiple testing, there is a 100% chance that the result (the logFC here) is due to chance.</p>
  <ol start="3">
  <li>You are correct. The expression of <code>Cttnbp2</code> donwn-regulated by that factor. If you were to look in the table at the cluster 1 DE genes you would see <code>Cttnbp2</code> with a logFC value of 1.35264. When you are looking at genes differentailly expressed in only two clusters, the sign is the only thing that changes.</li>
  </ol>
  <p><a href="https://satijalab.org/seurat/de_vignette.html" rel="nofollow noreferrer">Vignette</a> posted above by @heathobrien.</p>
  