text: user285: 3 Control replicate and 2 test sample ,so Im comparing my Control which is my Progenitor cells to Monocyte which is mature stage
  this is my code im using
  condition <- factor(c(rep("Control", 3),rep("Test", 2)),levels=c("Control", "Test"))
  
  
  (coldata <- data.frame(row.names=colnames(countdata), condition))
  dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
  
  This is my deseq2 output 
  gene baseMean log2FoldChange lfcSE  stat pvalue padj CB1 CB2 CB3 GD5_1  GD5_2
  ENSG00000144655 2030.6146124999 -5.0812043868   0.1183868766    -42.9203348727  0   0   3327.4890036209 3267.1877800456 3362.7407570783 98.5079578403   97.1475639145
  
  Im not sure how come the pvalue and  padj is 0? even though the sample value there is a difference and there is also fold change ,something wrong with the result ? 
  
  user581: A p-value of 0 is expected in this case. The p-values are calculated by comparing the Wald stat to a standard normal, so you can confirm that this is correct like this:
  > pnorm(-42.9203348727)
  [1] 0
  
  It really means p < 2.225074e-308 See here for a more details
  
original_text: 285: <p>3 Control replicate and 2 test sample ,so Im comparing my Control which is my Progenitor cells to Monocyte which is mature stage</p>
  
  <p>this is my code im using</p>
  
  <pre><code>condition &lt;- factor(c(rep("Control", 3),rep("Test", 2)),levels=c("Control", "Test"))
  
  
  (coldata &lt;- data.frame(row.names=colnames(countdata), condition))
  dds &lt;- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
  </code></pre>
  
  <p>This is my deseq2 output </p>
  
  <pre><code>gene baseMean log2FoldChange lfcSE  stat pvalue padj CB1 CB2 CB3 GD5_1  GD5_2
  ENSG00000144655 2030.6146124999 -5.0812043868   0.1183868766    -42.9203348727  0   0   3327.4890036209 3267.1877800456 3362.7407570783 98.5079578403   97.1475639145
  </code></pre>
  
  <p>Im not sure how come the pvalue and  padj is 0? even though the sample value there is a difference and there is also fold change ,something wrong with the result ? </p>
   581: <p>A p-value of 0 is expected in this case. The p-values are calculated by comparing the Wald stat to a standard normal, so you can confirm that this is correct like this:</p>
  
  <pre><code>&gt; pnorm(-42.9203348727)
  [1] 0
  </code></pre>
  
  <p>It really means p &lt; 2.225074e-308 See <a href="https://support.bioconductor.org/p/64787" rel="nofollow noreferrer">here</a> for a more details</p>
  