title: Plotting gene expression data with means in a randomized experiment
body: <p>I'm (a newbie to R) analyzing a randomized study on the effect of two treatments on gene expression. We evaluated 5 different genes at baseline and after 1 year. The gene fold is calculated as the value at 1 year divided by the baseline value.</p>
  
  <p>Example gene:
  IL10_BL
  IL10_1Y
  IL10_fold</p>
  
  <p>Gene expression is measured as a continuous variable, typically ranging from 0.1 to 5.0.
  100 patients have been randomized to either a statin or diet regime.</p>
  
  <p>I would like to do the following plot:
  - Y axis should display the mean gene expression with 95% confidence limit
  - X axis should be categorical, with the baseline, 1 year and fold value for each of the 5 genes, grouped by treatment. So, 5 genes with 3 values for each gene in two groups would mean 30 categories on the X axis. It would be really nice of the dots for the same gene would be connected with a line.</p>
  
  <p>I have tried to do this myself (using ggplot2) without any success. I've tried to do it directly from the crude data, which looks like this (first 6 observations and 2 different genes):</p>
  
  <pre><code>    genes &lt;- read.table(header=TRUE, sep=";", text = 
      "treatment;IL10_BL;IL10_1Y;IL10_fold;IL6_BL;IL6_1Y;IL6_fold;
      diet;1.1;1.5;1.4;1.4;1.4;1.1;
      statin;2.5;3.3;1.3;2.7;3.1;1.1;
      statin;3.2;4.0;1.3;1.5;1.6;1.1;
      diet;3.8;4.4;1.2;3.0;2.9;0.9;
      statin;1.1;3.1;2.8;1.0;1.0;1.0;
      diet;3.0;6.0;2.0;2.0;1.0;0.5;")
  </code></pre>
  
  <p>I would greatly appreciate any help (or link to a similar thread) to do this.</p>