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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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Concern about the P value! #186

Open M-Chi-1 opened 1 year ago

M-Chi-1 commented 1 year ago

Hi,

I have concern about the dff table, How does the P value calculated? I have 2 time points in my experiment, one of them (9_hpi) only and has one replicate. The another time point is (24_hpi) and has 2 replicates. Does the replicate reflect the significant positions in both or one replicate? Please see the attached and I hope this make sense. Thanks in advance.

xpore_2023-09-23 at 20 15 01 xpore_2023-09-23 at 20 07 54
yuukiiwa commented 1 year ago

Hi @M-Chi-1,

xpore calculates the p-value based on the sample groups provided (you can provide whatever number of replicates in each sample group).

If your sample group has one replicate (your 9_hpi time point) then the p-value reflects that the position is significant in one replicate. As your 24_hpi time point has two replicates in each sample group, then the position is significant in two replicates.

Thanks!

Best wishes, Yuk Kei