text: user4595: I have a gene expression raw counts like below for 16 patients 
           A  B    C      D   E   F
  A2M     511 1623 665    208 553 469
  AADAT   34  137 372     7   52  124
  ABCB1   119 114 123    22   25  89
  ABCB11  27  186 200    27   30  49
  ABCC2   1   10  21     1    8   3
  
  For each patients I also have some characteristics 
  Patients                          IC          TCs
  A1                                3            3
  B1                                2            0
  C1                                2            0
  D1                                0            0
  
  I want to find genes differential expressed in these patients regarding these characteristics but I don't know how to do that
  Any help please?
  
  user2388: Look up a tutorial on DESeq2.  To keep things simple for your first time, I'd reduce your phenotypes to "high" and "low" bins instead of trying to use the cell count numbers as they are.  Then once you understand what the software is doing, you can get fancier.
  
original_text: 4595: <p>I have a gene expression raw counts like below for 16 patients </p>
  
  <pre><code>         A  B    C      D   E   F
  A2M     511 1623 665    208 553 469
  AADAT   34  137 372     7   52  124
  ABCB1   119 114 123    22   25  89
  ABCB11  27  186 200    27   30  49
  ABCC2   1   10  21     1    8   3
  </code></pre>
  
  <p>For each patients I also have some characteristics </p>
  
  <pre><code>Patients                          IC          TCs
  A1                                3            3
  B1                                2            0
  C1                                2            0
  D1                                0            0
  </code></pre>
  
  <p>I want to find genes differential expressed in these patients regarding these characteristics but I don't know how to do that</p>
  
  <p>Any help please?</p>
   2388: <p>Look up a tutorial on DESeq2.  To keep things simple for your first time, I'd reduce your phenotypes to "high" and "low" bins instead of trying to use the cell count numbers as they are.  Then once you understand what the software is doing, you can get fancier.</p>
  