I don't understand this warning when I calculate the TMM factors. Is it going to affect downstream analysis?
corrected = pycombat_seq(counts, sampleinfo['Sample.supplying.institution'])
corrected=pd.DataFrame(corrected, columns=Samples, index=genes_in_counts['ensembl_gene_id'])
norm_factors= tmm_norm_factors(corrected)
cpm = conorm.cpm(corrected, norm_factors=norm_factors)
WARNING:py.warnings:<ipython-input-39-d0d30050dc7b>:1: DeprecationWarning: the `interpolation=` argument to
nanquantile was renamed to `method=`, which has additional options.
Users of the modes 'nearest', 'lower', 'higher', or 'midpoint' are encouraged to review the method they used.
(Deprecated NumPy 1.22)
norm_factors= tmm_norm_factors(corrected)
•
written
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Shaimaa Gamal •
1 answer
It is impossible to know whether this will affect the downstream analysis without digging through the code. It may help if you ask the author(s) directly.
It appears that you have a more recent NumPy version where some of the options have changed. Short of you correcting the code directly to account for these changes, it seems that the best course of action would be to downgrade NumPy to whatever version is needed by the program. If this is done in a general environment where NumPy can't be changed, you can try this on some old data where the output is known and compare with what you get now.
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