title: Performing a 2 sample t test in R with replicates
body: <p>I have a dataframe name R_alltemp in R with 6 columns, 2 groups of data with 3 replicates each. I'm trying to perform a t-test for each row between the first three values and the last three and use apply() so it can go through all the rows with one line. Here is the code im using so far.</p>
  
  <pre><code>R_alltemp$p.value&lt;-apply(R_all3,1, function (x) t.test(x(R_alltemp[,1:3]), x(R_alltemp[,4:6]))$p.value)
  </code></pre>
  
  <p>and here is a snapshot of the table</p>
  
  <pre><code>    R1.HCC827  R2.HCC827  R3.HCC827 R1.nci.h1975 R2.nci.h1975 R3.nci.h1975  p.value
  1  13.587632  22.225083  15.074230    58.187465           79    82.287573 0.4391160
  2   2.717526   1.778007   1.773439     1.763257            2     1.679338 0.4186339
  3 203.814478 191.135711 232.320487   253.908939          263   263.656100 0.4904493
  4  44.386264  45.339169  54.089884     3.526513            3     5.877684 0.3095634
  </code></pre>
  
  <p>it functions, but the p-values im getting just from eyeballing it seem wrong. For instance in the first line, the average of the first group is way lower than the second group, but my p value is only .4.</p>
  
  <p>I feel like I'm missing something very obvious here, but I've been struggling with it for much longer than I'd like. Any help would be appreciated.</p>