mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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QQ plot graphs #222

Closed AlperYurtseven closed 1 year ago

AlperYurtseven commented 1 year ago

Hi, After following the tutorial, we have ended up having qq plots like this for our data. What can we interpret from these two graphs? qq_plot qq_plot (1) Thank you in advance

johnlees commented 1 year ago

From the documentation:

When interpreting this plot, check that it is well controlled at low p-values and doesn’t show any large ‘shelves’ symptomatic of poorly controlled confounding population structure. Although this plot is far above the null (as indeed, there are many k-mers associated with penicillin resistance), the p-values up to 0.01 are as expected which is what we’re after.

These look ok to me