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    <p>Your names end with 'df', which makes it seem like your data are a data.frame. But @Troy's answer uses a matrix. A matrix is appropriate when the data are homogeneous, and generally matrix operations are much faster than data.frame operations. So you can see already that if you'd provided a small example of your data set (e.g., <code>dput(mRNAdf[1:10,])</code> that people might be in a better position to help you; this is what they're asking for.</p> <p>In large numerical calculations it makes sense to 'hoist' any repeated calculations outside the loop, so they are performed only once. Repeated calculations in your case include sub-setting to columns 2:13, and coercion to numeric. With this idea, and guessing that you actually have a data.frame where each column is already a numeric vector, I'd start with</p> <pre><code>mRNAmatrix &lt;- as.matrix(mRNAdf[,2:13]) miRmatrix &lt;- as.matrix(miRdf[,2:13]) </code></pre> <p>From the help page <code>?cor</code> we see that the arguments can be a matrix, and if so the correlation is calculated between columns. You're interested in the result when the arguments are transposed relative to your current representation. So</p> <pre><code>result &lt;- cor(t(mRNAmatrix), t(miRmatrix), use="complete.obs") </code></pre> <p>This is fast enough for your purposes</p> <pre><code>&gt; m1 = matrix(rnorm(71521 * 12), 71521) &gt; m2 = matrix(rnorm(1477 * 12), 1477) &gt; system.time(ans &lt;- cor(t(m1), t(m2))) user system elapsed 9.124 0.200 9.340 &gt; dim(ans) [1] 71521 1477 </code></pre> <p><code>result</code> is the same as your <code>corrList</code> -- it's not a list, but a matrix; probably the row and column names have been carried forward. You'd write this to a file as you do above, <code>write.csv(result, "testCorrWhole.csv")</code></p>
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    1. USMartin Morgan
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    1. COThanks! So in the code above, where is the script that outputs the individual cor scores into an "output" data frame? Sorry if I am not understanding fully.
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    2. COI've updated my reply. The result is in a matrix, not a data.frame (in your code too, I think) and can be written to a file with `write.csv`.
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    3. COThat code went from taking 14hrs (the way I had it written) to 45 seconds your way. I cant thank you enough!
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