Mark mentioned that methylprep was reordering the probes during processing. It might be this pandas dataframe bug:
Warning (from warnings module):
File “/Users/mmaxmeister/legx/test_combine_mds.py”, line 302
slice_betas = pd.concat([slice_betas, betas[sample]], axis=1)
FutureWarning: Sorting because non-concatenation axis is not >aligned. A future version of pandas will change to not sort by default.
To accept the future behavior, pass ‘sort=False’.
To retain the current behavior and silence the warning, pass ‘sort=True’.
I’m sure I accepted the (sort=True) part to suppress the warning, but as a result, it is reordering the probes. Will put this as an issue.
Mark mentioned that methylprep was reordering the probes during processing. It might be this pandas dataframe bug:
I’m sure I accepted the (sort=True) part to suppress the warning, but as a result, it is reordering the probes. Will put this as an issue.