text: user13950: What does the padj really mean? I believe it's a BH method, where it attempts to quantify the likelihood of a "false positive" but I am not sure. Also, what does it mean if the resulting calculations nearly all have the same padj values despite having different p-values?
  
  user2108: If we look at documentation of DESEQ2 and search "adjusted p-value", we find the section "Multiple test correction". In this section they discuss Benjamini-Hochberg ("BH") false discovery rate (FDR) correction procedures:
  
  FDR/Benjamini-Hochberg: Benjamini and Hochberg (1995) defined the concept of FDR and created an algorithm to control the expected FDR below a specified level given a list of independent p-values. An interpretation of the BH method for controlling the FDR is implemented in DESeq2 in which we rank the genes by p-value, then multiply each ranked p-value by m/rank.
  
  Earlier, they write:
  
  m = total number of tests
  
  They further add:
  
  So what does FDR < 0.05 mean? By setting the FDR cutoff to < 0.05, we’re saying that the proportion of false positives we expect amongst our differentially expressed genes is 5%. For example, if you call 500 genes as differentially expressed with an FDR cutoff of 0.05, you expect 25 of them to be false positives.
  
  I would suggest reading Benjamini and Hochberg (1995) to learn more details if desired.
  
original_text: 13950: <p>What does the padj really mean? I believe it's a BH method, where it attempts to quantify the likelihood of a &quot;false positive&quot; but I am not sure. Also, what does it mean if the resulting calculations nearly all have the same padj values despite having different p-values?</p>
   2108: <p>If we look at <a href="https://hbctraining.github.io/DGE_workshop/lessons/05_DGE_DESeq2_analysis2.html" rel="nofollow noreferrer">documentation of DESEQ2</a> and search &quot;adjusted p-value&quot;, we find the section &quot;Multiple test correction&quot;. In this section they discuss Benjamini-Hochberg (&quot;BH&quot;) false discovery rate (FDR) correction procedures:</p>
  <blockquote>
  <p>FDR/Benjamini-Hochberg: Benjamini and Hochberg (1995) defined the concept of FDR and created an algorithm to control the expected FDR below a specified level given a list of independent p-values. <strong>An interpretation of the BH method for controlling the FDR is implemented in DESeq2 in which we rank the genes by p-value, then multiply each ranked p-value by m/rank.</strong></p>
  </blockquote>
  <p>Earlier, they write:</p>
  <blockquote>
  <p>m = total number of tests</p>
  </blockquote>
  <p>They further add:</p>
  <blockquote>
  <p>So what does FDR &lt; 0.05 mean? By setting the FDR cutoff to &lt; 0.05, we’re saying that the proportion of false positives we expect amongst our differentially expressed genes is 5%. For example, if you call 500 genes as differentially expressed with an FDR cutoff of 0.05, you expect 25 of them to be false positives.</p>
  </blockquote>
  <p>I would suggest reading Benjamini and Hochberg (1995) to learn more details if desired.</p>
  