User: jgranek

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jgranek0
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Posts by jgranek

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biomformat::make_biom roundtrip problem?
... The Example from ?biomformat::make_biom is not behaving as I expect - I assume that this is a bug, but perhaps I am not understanding the example. The example seems to imply that the components should be identical after writing BIOM files, then reading them back in, but the sample and observation me ...
biomformat written 20 months ago by jgranek0
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Comment: C: Fold Change Not Monotonic With Counts
... OK, that sheds some light on it,  I first wondered if the rows with seemingly incorrect FC values were having problems because they were outliers. But then noticed that small changes in input resulted in more sensible FC values, which smelled like an edge case bug.  For example count.df = data.frame ...
written 3.7 years ago by jgranek0
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Comment: C: Fold Change Not Monotonic With Counts
... Oops sorry, this example is monotonically decreasing, which also seems to be a problem.  I would expect that if gene1$WT == gene2$WT and  gene1$MUT < gene2$MUT, then FC(gene1) < FC(gene2).  But here FC(gene1) > FC(gene2). I do have less minimal datasets that DO show non-monotonicity, but I ...
written 3.7 years ago by jgranek0
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Comment: C: Fold Change Not Monotonic With Counts
... OK, updated example code to be less verbose, and hopefully more clear ...
written 3.7 years ago by jgranek0
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Fold Change Not Monotonic With Counts
... I have found some cases where the fold change values don't make sense to me, and I am wondering if I hit some edge case bug.  Here is one example, notice that row 3 has more MUT1 counts than rows 1 and 2, but a lower fold change.  WT_1 MUT_1 log2FoldChange 1 0 3 2.348419e+00 2 0 ...
deseq2 written 3.7 years ago by jgranek0

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