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POpaired t-test crashes apply-loop (edited)
 

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  1. POpaired t-test crashes apply-loop (edited)
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    <p><strong>In response to the helpful comments, I have edited the original question (where I had assumed that a for-loop and an apply-loop give different results).</strong></p> <p>I am using R to run a large number of 2-group t-tests, using input from a delimited table. Following recommendations from here and elsewhere, I tried either 'for-loops' and 'apply' to accomplish that. For 'normal' t.test, both work nicely and give the same results. However, for a paired t-test, the for-look appears to works while the apply-loop does not. Later, i found out that both loops suffer from the same problem (see below) but the for-loops deals more gracefully with the situation (only one cycle of the loop returns an invalid result) while the apply-loop fails altogether.</p> <p>My input file looks like this: (the first line is a header line, the data lines have a name, 4 datapoints for group 1 and 4 datapoints for group 2):</p> <pre><code>header g1.1 g1.2 g1.3 g1.4 g2.1 g2.2 g2.3 g2.4 name1 0 0.5 -0.2 -0.2 -0.1 0.4 -0.3 -0.3 name2 23.2 24.4 24.5 27.2 15.5 16.5 17.7 20.0 name3 ..... </code></pre> <p>and so on (overall ~50000 lines). The first data line (starting with name19 turned out to be the culprit.</p> <p>This is the for-loop version that works better (failes on the problematic line but correctly deals with all other lines):</p> <pre><code>table &lt;- read.table('ttest_in.txt',head=1,sep='\t') for(i in 1:nrow(table)) { g1&lt;-as.numeric((table)[i,2:5]) g2&lt;-as.numeric((table)[i,6:9]) pv &lt;- t.test(g1,g2,paired=TRUE)$p.value } </code></pre> <p>This is the 'apply' version that causes problems</p> <pre><code>table &lt;- read.table('ttest_in.txt',head=1,sep='\t') pv.list &lt;- apply(table[,2:9],1,function(x){t.test(x[1:4],x[5:8],paired=TRUE)$p.value}) </code></pre> <p>One of the ~50000 data lines is problematic in that the differences of all pairwise comparions are identical, which in a paired t-test results in an undefined p-value (essentially zero). The apply loop crashes with the error 'data are essentially constant'. To me (as an R newbie) it does not seem to be a good idea to crash the entire script just because the t.test doesn't like one piece of data. In the for-loop, this data line also results in an error message but the loop continues and all the other t-tests give correct results.</p> <p>Did I do something fundamentally wrong? This behaviour a essentially prohibits the usage of apply-loops for this kind of batch analysis. Or is there a standard way to circumvent this problem. Why doesn't the t-test just return something invalid for that particular p-value instead of bailing out?</p>
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    1. USuser900889
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    1. COCan you provide a minimal example reproducing the error? We probably need more help than you give us above. However, don't do the `as.matrix()` line in the `apply()` version. If `header` is really in the file then you may be getting into trouble there. `apply()` works on a data frame just fine, so you can use `pv.list <- apply(table[, 2:9], 1 ,function(x) { t.test(x[1:4], x[5:8], paired=TRUE)$p.value})` rather than work on the matrix `mat`. Does that fix things?
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      1. POpaired t-test crashes apply-loop (edited)
      1. USGavin Simpson
    2. COTo add to Gavin's excellent questions: try running your `apply` code with `debug` turned on. Some semi-obvious indexing error may show up.
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      1. POpaired t-test crashes apply-loop (edited)
      1. USCarl Witthoft
    3. COThanks for your comments. Gavin's suggestion to skip the as.matrix step simplified the script but did not change anything. I am not familiar with 'debug', I might try this later. Next, I tracked down the culprit line and now i (partially) undestand the problem. I have changed the example file above, it is the first line that causes the problem. I can see why a paired t-test doesn't like these data, but is this reason enough to crash the entire 'apply' loop? Is there anything I can do about this?
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