My data contains 20samples(10samples per group, two groups) and 481 features,
I imported ancom funtion from skbio, here are my codes:
from skbio.stats.composition import ancom
from scipy.stats import ttest_ind
ancom_none, ancom_none_pct = ancom(table=table, grouping=grouping, significance_test=ttest_ind, multiple_comparisons_correction=None)
===> 5 features were significantly different between 2 groups. Here are the W value of some features:
ancom_none, ancom_none_pct = ancom(table=table, grouping=grouping, significance_test=ttest_ind, multiple_comparisons_correction=‘holm-bonferroni’)
===> I prefered to do the correction, so I set multiple_comparisons_correction to be ‘holm-bonferroni’, nothing else changed. But now all features rejected the null hypothesis, so they were all significantly different between two groups, while the W value were pretty low. Same features with pic above:
The results were weird, could anyone give some suggestions?
Thanks in advance!