Compute function failing on c7<0.05 on DeSeq2 results

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I am working on rna seq analysis and am trying to add a T/F significant differential gene expression column onto my DeSeq2 results for use in goseq. Compute is failing when it gets to rows with NA listed as the p-value because it’s not converting the strings to floats, but even when I play with the error-handling options it is failing no matter what. I am using c7<0.05 as my function where c7 is the adj. p-value. I have already tried to Skip the Row & Produce an empty column to deal with the errors. TIA

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Hi @jbliss

When choosing an Error Handling option for the Compute on rows tool, the last 2 of the 3 options go together.

That means if you are setting a non-default option for If an expression cannot be computed for a row, make sure that the option right above it Fail on references to non-existent columns is set to NO.

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THANK YOU!!! I knew it had to be something simple and I wasn’t clicking all the right settings together. The Training Material is super helpful-- thank you so much for sharing!

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@jbliss glad to hear that the GTN was helpful.
@jennaj just to clarify how the different error handling options are interconnected:

  • the most important option with conversion errors like this is Autodetect column types.
    Conversion to the types Galaxy has recorded for all columns is otherwise the first thing the tool does, and this doesn’t count yet as trying to compute the expression. So if this step fails, that’s that.
  • after you’ve disabled the above option, you will have to use an extended expression that does the type conversion itself, like float(c7).
  • Now, in this case here, that attempt will also fail, but now the failure is part of computing the expression, and can be handled via If an expression cannot be computed for a row
  • Fail on references to non-existent columns does not matter in the case here because the column does exist, just its value cannot be converted to a float.
    You’re right, of course, that if a missing column is the issue, then you need to set this option to No and configure error handling at the same time.
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