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Weird bug when trying to normalize p-values #5
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Hi,
Could you send me the head of your curated dataset that you’re using as input. Also, the exact command you’re using when you encounter the error? I’ll be a little delayed but hopefully I can find some time this weekend to look into the code. Also, make sure there’s no NAs in your code. Once I figure out the bug, I can write a better error message.
Best,
Andrew
… On Jan 4, 2022, at 9:12 PM, Bérénice Benayoun ***@***.***> wrote:
Hi,
I am encountering a weird bug after inputting my data when I start the p-value normalization steps.
The annotateExpression and annotateModification steps work fine, so does the makePvalueObject step, and no errors occur. An object is generated.
Then, wen I attempt to proceed to pval normalization steps, things stop working unexpectedly and the error messages are not very helpful.
when calling plotDensityPval: ```
Error in abs(returnPvalueCol(slot(pvalue_annotation, "score_data"), ref)) :
non-numeric argument to mathematical function
- when calling normalizePval: `Error in 1 - p_ref : non-numeric argument to binary operator`
Any idea what is happening and how to fix it? I have tried reformatting, removing some of my epigenomics, etc, but nothing is changing the error message.
Thank you for your help!
Best
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Hi Andrew, thank you for the quick response! I have already checked, and there are no NAs or p-values equal to zero in our dataset. Here is the sequence of events that runs without error:
Then, the prior errors occur when I either run:
Here are the headers of my inputs:
perimac_enhancers[,1:3]
my.RNA.clean
F.my.atac.clean
Any insights to figure out why this is not running (when the test data runs without issue) would be greatly appreciated. Thank you! |
Hi,
I am encountering a weird bug after inputting my data when I start the p-value normalization steps.
The annotateExpression and annotateModification steps work fine, so does the makePvalueObject step, and no errors occur. An object is generated.
Then, wen I attempt to proceed to pval normalization steps, things stop working unexpectedly and the error messages are not very helpful.
when calling plotDensityPval:
Error in abs(returnPvalueCol(slot(pvalue_annotation, "score_data"), ref)) : non-numeric argument to mathematical function
when calling normalizePval:
Error in 1 - p_ref : non-numeric argument to binary operator
Any idea what is happening and how to fix it? I have tried reformatting, removing some of my epigenomics, etc, but nothing is changing the error message.
Thank you for your help!
Best
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