Closed mireiacodina closed 1 year ago
Hi @mireiacodina! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, how will we be able to help?
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I am sorry, I moved it to the discussions session as it is not an error from the code.
Hello, I met the same issue! Did you solve it or any comments? Thank you.
Hello,
Thanks for developing ArchR. I have a question related to the getMarkerfeatures() function to do pairwise testing between groups. I want to compare the accessibility between two cell types and I get different logFC and FDR values depending on the group that I use in useGroups and the one that I set as bgdGroups.
Here is the code that I run:
Also, the total number of significant peaks based on the cutoff that I used is different (3601 for sig_peaks and 4889 for sig_peaks2). I would be very thankful if I could get any feedback on why the results are different. I also tried running the code without the "bias" variable but it did not change the outcome.
Thank you very much.