text: user4595: I have a treatment and control in two time points like this
   > design
                                   X condition time
      1       CTRL_24_hrs_replicate1   control   24
      2       CTRL_24_hrs_replicate2   control   24
      3       CTRL_24_hrs_replicate3   control   24
      4  treatment_24_hrs_replicate1        t   24
      5  treatment_24_hrs_replicate2        t   24
      6  treatment_24_hrs_replicate3        t   24
      7       CTRL_48_hrs_replicate1   control   48
      8       CTRL_48_hrs_replicate2   control   48
      9       CTRL_48_hrs_replicate3   control   48
      10 treatment_48_hrs_replicate1        t   48
      11 treatment_48_hrs_replicate2        t   48
      12 treatment_48_hrs_replicate3        t   48
      > 
  
                                                 
      
  
  I want to test between between treatment and control considering time point 2 hours to 4 hours
  I have done like this
  dds <- DESeqDataSetFromMatrix(countData=a,colData=design, design=~time + condition + time:condition)
  
  ddsTC <- DESeq(dds, test="LRT", reduced = ~ time + time:condition)
  
  > resultsNames(ddsTC)
  [1] "Intercept"                "condition_t_vs_control"  
  [3] "time"                     "conditiont.time" 
  
   
  
  What is the difference of the results of these codes
  results(ddsTC, name="condition_t_vs_control", test="Wald")
  
  versus
  results(ddsTC, name="conditiont.time", test="Wald")
  
  Actually I want to know what condition_t_vs_control gives and what conditiont.time gives
  Thank you so much for any intuition
  
  user77: condition_t_vs_control gives the effect of condition, conditiont.time is the interaction of condition and time. If you wanted to test the effect of time, use name="time".
  
original_text: 4595: <p>I have a treatment and control in two time points like this</p>
  <pre><code> &gt; design
                                   X condition time
      1       CTRL_24_hrs_replicate1   control   24
      2       CTRL_24_hrs_replicate2   control   24
      3       CTRL_24_hrs_replicate3   control   24
      4  treatment_24_hrs_replicate1        t   24
      5  treatment_24_hrs_replicate2        t   24
      6  treatment_24_hrs_replicate3        t   24
      7       CTRL_48_hrs_replicate1   control   48
      8       CTRL_48_hrs_replicate2   control   48
      9       CTRL_48_hrs_replicate3   control   48
      10 treatment_48_hrs_replicate1        t   48
      11 treatment_48_hrs_replicate2        t   48
      12 treatment_48_hrs_replicate3        t   48
      &gt; 
  
                                                 
      
  </code></pre>
  <p>I want to test between between treatment and control considering time point 2 hours to 4 hours</p>
  <p>I have done like this</p>
  <pre><code>dds &lt;- DESeqDataSetFromMatrix(countData=a,colData=design, design=~time + condition + time:condition)
  
  ddsTC &lt;- DESeq(dds, test=&quot;LRT&quot;, reduced = ~ time + time:condition)
  
  &gt; resultsNames(ddsTC)
  [1] &quot;Intercept&quot;                &quot;condition_t_vs_control&quot;  
  [3] &quot;time&quot;                     &quot;conditiont.time&quot; 
  
   
  </code></pre>
  <p>What is the difference of the results of these codes</p>
  <pre><code>results(ddsTC, name=&quot;condition_t_vs_control&quot;, test=&quot;Wald&quot;)
  </code></pre>
  <p><strong>versus</strong></p>
  <pre><code>results(ddsTC, name=&quot;conditiont.time&quot;, test=&quot;Wald&quot;)
  </code></pre>
  <p>Actually I want to know what <code>condition_t_vs_control</code> gives and what <code>conditiont.time</code> gives</p>
  <p>Thank you so much for any intuition</p>
   77: <p><code>condition_t_vs_control</code> gives the effect of condition, <code>conditiont.time</code> is the interaction of condition and time. If you wanted to test the effect of time, use <code>name=&quot;time&quot;</code>.</p>
  