Differential regulation: ANOVA across more than two groups and posthoc t-tests

Differential regulation: ANOVA across more than two groups and posthoc t-tests#

This API example shows the functionality in the acore.differential_regulation module:

  • Analysis of Variance (ANOVA) as omnibus test across more than two groups

  • posthoc t-tests between each of the groups

An omnibus analysis across groups is combined with posthoc analysis between each set of the separate groups.

The function is the same as for the two groups case. The group1 and group2 columns give the posthoc comparison.

%pip install acore

Hide code cell output

 
Requirement already satisfied: acore in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (0.3.0)
Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.4.6)
Requirement already satisfied: pandas in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.3.3)
Requirement already satisfied: dsp-pandas in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.0.5)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.17.1)
Requirement already satisfied: scikit-learn>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.9.0)
Requirement already satisfied: gseapy!=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.2.1)
Requirement already satisfied: pingouin<0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.5.5)
Requirement already satisfied: umap-learn in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.5.12)
Requirement already satisfied: statsmodels in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.14.6)
Requirement already satisfied: combat in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.3.3)
Requirement already satisfied: inmoose in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.9.1)
Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.34.2)
Requirement already satisfied: rarfile in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (4.2)
Requirement already satisfied: pandera in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.31.1)
Requirement already satisfied: matplotlib in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (3.11.0)
Requirement already satisfied: pandas-flavor in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.8.1)
Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.13.2)
Requirement already satisfied: tabulate in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.10.0)
Requirement already satisfied: contourpy>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (1.3.3)
Requirement already satisfied: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (4.63.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (1.5.0)
Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (26.2)
Requirement already satisfied: pillow>=9 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (12.2.0)
Requirement already satisfied: pyparsing>=3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (3.3.2)
Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas->acore) (2026.2)
Requirement already satisfied: tzdata>=2022.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas->acore) (2026.2)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib->pingouin<0.6.0->acore) (1.17.0)
Requirement already satisfied: joblib>=1.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (1.5.3)
Requirement already satisfied: narwhals>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (2.22.1)
Requirement already satisfied: threadpoolctl>=3.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (3.6.0)
Requirement already satisfied: mpmath>=1.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from combat->acore) (1.4.1)
Requirement already satisfied: patsy>=0.5.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from combat->acore) (1.0.2)
Requirement already satisfied: openpyxl in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dsp-pandas->acore) (3.1.5)
Requirement already satisfied: anndata in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from inmoose->acore) (0.12.17)
Requirement already satisfied: fastcluster in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from inmoose->acore) (1.3.0)
Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from inmoose->acore) (3.1.6)
Requirement already satisfied: array-api-compat>=1.7.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (1.15.0)
Requirement already satisfied: h5py>=3.8 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (3.16.0)
Requirement already satisfied: legacy-api-wrap in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (1.5)
Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (8.4.0)
Requirement already satisfied: scverse-misc>=0.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (0.0.3)
Requirement already satisfied: zarr!=3.0.*,>=2.18.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (3.1.6)
Requirement already satisfied: session-info2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scverse-misc>=0.0.3->anndata->inmoose->acore) (0.4.1)
Requirement already satisfied: typing-extensions in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scverse-misc>=0.0.3->anndata->inmoose->acore) (4.15.0)
Requirement already satisfied: donfig>=0.8 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (0.8.1.post1)
Requirement already satisfied: google-crc32c>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (1.8.0)
Requirement already satisfied: numcodecs>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (0.16.5)
Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from donfig>=0.8->zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (6.0.3)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jinja2->inmoose->acore) (3.0.3)
Requirement already satisfied: et-xmlfile in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from openpyxl->dsp-pandas->acore) (2.0.0)
Requirement already satisfied: xarray in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas-flavor->pingouin<0.6.0->acore) (2026.4.0)
Requirement already satisfied: pydantic in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandera->acore) (2.13.4)
Requirement already satisfied: typeguard in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandera->acore) (4.5.2)
Requirement already satisfied: typing_inspect>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandera->acore) (0.9.0)
Requirement already satisfied: mypy-extensions>=0.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from typing_inspect>=0.6.0->pandera->acore) (1.1.0)
Requirement already satisfied: annotated-types>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->pandera->acore) (0.7.0)
Requirement already satisfied: pydantic-core==2.46.4 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->pandera->acore) (2.46.4)
Requirement already satisfied: typing-inspection>=0.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->pandera->acore) (0.4.2)
Requirement already satisfied: charset_normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (3.4.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (3.18)
Requirement already satisfied: urllib3<3,>=1.26 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (2.7.0)
Requirement already satisfied: certifi>=2023.5.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (2026.5.20)
Requirement already satisfied: numba>=0.51.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from umap-learn->acore) (0.65.1)
Requirement already satisfied: pynndescent>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from umap-learn->acore) (0.6.0)
Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from umap-learn->acore) (4.68.2)
Requirement already satisfied: llvmlite<0.48,>=0.47.0dev0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from numba>=0.51.2->umap-learn->acore) (0.47.0)
Note: you may need to restart the kernel to use updated packages.

Hide code cell source

 
import dsp_pandas
import pandas as pd

import acore.differential_regulation as ad

dsp_pandas.format.set_pandas_options(
    max_columns=9,
    max_colwidth=20,
)

BASE = (
    "https://raw.githubusercontent.com/Multiomics-Analytics-Group/acore/"
    "main/example_data/MTBLS13311/"
)
fname: str = "MTBLS13411_omics_and_meta.csv"  # combined omics and meta data
covariates: list[str] = []
group: str = "group"
drop_cols: list[str] = ["Factor Value[Strain type]"]
subject_col: str | int = 0
factor_and_covars: list[str] = [group, *covariates]

ANOVA analysis for two groups#

Use combined dataset for ANOVA analysis.

Hide code cell source

 
omics_and_meta = (
    pd.read_csv(f"{BASE}/{fname}", index_col=subject_col)
    .convert_dtypes()
    .dropna(subset=factor_and_covars)
)
omics_and_meta
Factor Value[Strain type] group Uracil Adenine ... Fructose 1,6-bisphosphate Arginine Ornithine Lysine
rapZE227Stop-1 phage-resistant rapZE227Stop 26.271 21.874 ... 20.164 23.718 25.082 22.330
rapZE227Stop-2 phage-resistant rapZE227Stop 27.293 21.983 ... 20.355 23.611 25.016 21.867
rapZE227Stop-3 phage-resistant rapZE227Stop 26.788 21.833 ... 20.331 23.834 25.158 21.729
rapZE227Stop-4 phage-resistant rapZE227Stop 27.014 22.120 ... 20.545 23.634 24.943 21.525
rapZE227Stop-5 phage-resistant rapZE227Stop 26.364 21.957 ... 20.208 23.971 25.206 22.180
rapZE227Stop-6 phage-resistant rapZE227Stop 26.571 21.885 ... 20.324 23.917 25.163 21.768
WT-1 Wild Type WT 26.472 21.826 ... 20.368 24.265 25.163 21.638
WT-2 Wild Type WT 26.325 21.652 ... 20.385 24.175 25.260 21.040
WT-3 Wild Type WT 26.274 21.651 ... 20.407 24.244 25.090 21.393
WT-4 Wild Type WT 26.187 21.780 ... 20.605 24.218 25.216 21.399
WT-5 Wild Type WT 26.244 21.702 ... 20.392 24.384 25.164 21.348
WT-6 Wild Type WT 26.313 21.770 ... 20.455 24.136 25.156 21.379
WRP-1 phage-resistant WRP 26.301 22.169 ... 20.205 23.923 25.111 21.752
WRP-2 phage-resistant WRP 25.721 21.546 ... 20.523 23.822 24.924 21.126
WRP-3 phage-resistant WRP 26.929 21.612 ... 20.513 23.828 24.917 21.084
WRP-4 phage-resistant WRP 26.265 21.738 ... 20.533 23.843 24.988 21.132
WRP-5 phage-resistant WRP 26.279 21.596 ... 20.555 23.871 25.063 21.508
WRP-6 phage-resistant WRP 26.550 21.626 ... 20.514 23.927 25.011 21.180
QC-1 <NA> QC 26.321 21.572 ... 20.339 24.129 25.139 21.544
QC-2 <NA> QC 26.289 21.511 ... 20.324 24.052 25.049 21.564
QC-3 <NA> QC 26.287 21.556 ... 20.331 24.066 25.097 21.513

21 rows × 61 columns

Drop unnecessary columns, if there are any specified in drop_cols.

Hide code cell source

 
if drop_cols:
    omics_and_meta.drop(columns=drop_cols, inplace=True)
omics_and_meta
group Uracil Adenine Hypoxanthine ... Fructose 1,6-bisphosphate Arginine Ornithine Lysine
rapZE227Stop-1 rapZE227Stop 26.271 21.874 23.201 ... 20.164 23.718 25.082 22.330
rapZE227Stop-2 rapZE227Stop 27.293 21.983 23.357 ... 20.355 23.611 25.016 21.867
rapZE227Stop-3 rapZE227Stop 26.788 21.833 23.167 ... 20.331 23.834 25.158 21.729
rapZE227Stop-4 rapZE227Stop 27.014 22.120 23.517 ... 20.545 23.634 24.943 21.525
rapZE227Stop-5 rapZE227Stop 26.364 21.957 23.246 ... 20.208 23.971 25.206 22.180
rapZE227Stop-6 rapZE227Stop 26.571 21.885 23.121 ... 20.324 23.917 25.163 21.768
WT-1 WT 26.472 21.826 22.980 ... 20.368 24.265 25.163 21.638
WT-2 WT 26.325 21.652 22.925 ... 20.385 24.175 25.260 21.040
WT-3 WT 26.274 21.651 22.885 ... 20.407 24.244 25.090 21.393
WT-4 WT 26.187 21.780 22.938 ... 20.605 24.218 25.216 21.399
WT-5 WT 26.244 21.702 22.945 ... 20.392 24.384 25.164 21.348
WT-6 WT 26.313 21.770 22.851 ... 20.455 24.136 25.156 21.379
WRP-1 WRP 26.301 22.169 23.295 ... 20.205 23.923 25.111 21.752
WRP-2 WRP 25.721 21.546 22.771 ... 20.523 23.822 24.924 21.126
WRP-3 WRP 26.929 21.612 22.696 ... 20.513 23.828 24.917 21.084
WRP-4 WRP 26.265 21.738 22.881 ... 20.533 23.843 24.988 21.132
WRP-5 WRP 26.279 21.596 22.861 ... 20.555 23.871 25.063 21.508
WRP-6 WRP 26.550 21.626 22.849 ... 20.514 23.927 25.011 21.180
QC-1 QC 26.321 21.572 22.779 ... 20.339 24.129 25.139 21.544
QC-2 QC 26.289 21.511 22.681 ... 20.324 24.052 25.049 21.564
QC-3 QC 26.287 21.556 22.732 ... 20.331 24.066 25.097 21.513

21 rows × 60 columns

Check data types of the columns. Metadata can be numeric, but also strings.

Hide code cell source

 
omics_and_meta.dtypes.value_counts()

Float64          59
string[python]    1
Name: count, dtype: int64

Hide code cell source

 
omics_and_meta[factor_and_covars]
group
rapZE227Stop-1 rapZE227Stop
rapZE227Stop-2 rapZE227Stop
rapZE227Stop-3 rapZE227Stop
rapZE227Stop-4 rapZE227Stop
rapZE227Stop-5 rapZE227Stop
rapZE227Stop-6 rapZE227Stop
WT-1 WT
WT-2 WT
WT-3 WT
WT-4 WT
WT-5 WT
WT-6 WT
WRP-1 WRP
WRP-2 WRP
WRP-3 WRP
WRP-4 WRP
WRP-5 WRP
WRP-6 WRP
QC-1 QC
QC-2 QC
QC-3 QC

With four groups#

Acore make each combinatorial comparison between groups in the group column.

if isinstance(subject_col, int):
    subject_col = omics_and_meta.index.name
anova = (
    ad.run_anova(
        omics_and_meta,  # .reset_index(),
        subject=subject_col,
        drop_cols=[],
        group=group,
    ).set_index(["identifier", "group1", "group2"])
    # .sort_values(by="padj")
)
anova.head().T
identifier Uracil
group1 QC WRP
group2 WRP WT rapZE227Stop WT rapZE227Stop
mean(group1) 26.299 26.299 26.299 26.341 26.341
std(group1) 0.019 0.019 0.019 0.396 0.396
mean(group2) 26.341 26.302 26.717 26.302 26.717
std(group2) 0.396 0.097 0.393 0.097 0.393
posthoc Paired False False False False False
posthoc Parametric True True True True True
posthoc T-Statistics -0.256 -0.076 -2.599 0.231 -1.651
posthoc dof 5.047 5.728 5.047 10.000 10.000
posthoc tail two-sided two-sided two-sided two-sided two-sided
posthoc pvalue 0.808 0.942 0.048 0.822 0.130
posthoc BF10 0.534 0.524 2.287 0.475 1.041
posthoc effsize -0.110 -0.034 -1.118 0.123 -0.880
log2FC -0.042 -0.003 -0.418 0.038 -0.376
FC 0.972 0.998 0.749 1.027 0.771
efftype hedges hedges hedges hedges hedges
F-statistics 2.441 2.441 2.441 2.441 2.441
pvalue 0.100 0.100 0.100 0.100 0.100
padj 0.123 0.123 0.123 0.123 0.123
correction FDR correction BH FDR correction BH FDR correction BH FDR correction BH FDR correction BH
rejected False False False False False
-log10 pvalue 0.093 0.026 1.320 0.085 0.887
Method One-way anova One-way anova One-way anova One-way anova One-way anova
posthoc padj 0.860 0.958 0.110 0.836 0.219

pairwise t-test results:#

cols_pairwise_ttest = [
    # "group1",
    # "group2",
    "mean(group1)",
    "std(group1)",
    "mean(group2)",
    "std(group2)",
    "posthoc Paired",
    "posthoc Parametric",
    "posthoc T-Statistics",
    "posthoc dof",
    "posthoc tail",
    "posthoc pvalue",
    "posthoc BF10",
    "posthoc effsize",
    # "identifier",
    "log2FC",
    "FC",
    "efftype",
]
anova[cols_pairwise_ttest]
mean(group1) std(group1) mean(group2) std(group2) ... posthoc effsize log2FC FC efftype
identifier group1 group2
Uracil QC WRP 26.299 0.019 26.341 0.396 ... -0.110 -0.042 0.972 hedges
WT 26.299 0.019 26.302 0.097 ... -0.034 -0.003 0.998 hedges
rapZE227Stop 26.299 0.019 26.717 0.393 ... -1.118 -0.418 0.749 hedges
WRP WT 26.341 0.396 26.302 0.097 ... 0.123 0.038 1.027 hedges
rapZE227Stop 26.341 0.396 26.717 0.393 ... -0.880 -0.376 0.771 hedges
... ... ... ... ... ... ... ... ... ... ... ...
Lysine QC WT 21.540 0.025 21.366 0.191 ... 0.957 0.175 1.129 hedges
rapZE227Stop 21.540 0.025 21.900 0.301 ... -1.256 -0.359 0.779 hedges
WRP WT 21.297 0.271 21.366 0.191 ... -0.271 -0.069 0.953 hedges
rapZE227Stop 21.297 0.271 21.900 0.301 ... -1.945 -0.603 0.658 hedges
WT rapZE227Stop 21.366 0.191 21.900 0.301 ... -1.957 -0.534 0.691 hedges

354 rows × 15 columns

ANOVA results

anova.drop(columns=cols_pairwise_ttest)
F-statistics pvalue padj correction rejected -log10 pvalue Method posthoc padj
identifier group1 group2
Uracil QC WRP 2.441 0.100 0.123 FDR correction BH False 0.093 One-way anova 0.860
WT 2.441 0.100 0.123 FDR correction BH False 0.026 One-way anova 0.958
rapZE227Stop 2.441 0.100 0.123 FDR correction BH False 1.320 One-way anova 0.110
WRP WT 2.441 0.100 0.123 FDR correction BH False 0.085 One-way anova 0.836
rapZE227Stop 2.441 0.100 0.123 FDR correction BH False 0.887 One-way anova 0.219
... ... ... ... ... ... ... ... ... ... ...
Lysine QC WT 7.393 0.002 0.005 FDR correction BH True 1.121 One-way anova 0.104
rapZE227Stop 7.393 0.002 0.005 FDR correction BH True 1.490 One-way anova 0.083
WRP WT 7.393 0.002 0.005 FDR correction BH True 0.206 One-way anova 0.655
rapZE227Stop 7.393 0.002 0.005 FDR correction BH True 2.350 One-way anova 0.020
WT rapZE227Stop 7.393 0.002 0.005 FDR correction BH True 2.367 One-way anova 0.015

354 rows × 8 columns

Test results

Hide code cell source

 
regex_filter = "pval|padj|reject|stat|FC"
view = anova.filter(regex=regex_filter)
view
posthoc pvalue log2FC FC F-statistics pvalue padj rejected -log10 pvalue posthoc padj
identifier group1 group2
Uracil QC WRP 0.808 -0.042 0.972 2.441 0.100 0.123 False 0.093 0.860
WT 0.942 -0.003 0.998 2.441 0.100 0.123 False 0.026 0.958
rapZE227Stop 0.048 -0.418 0.749 2.441 0.100 0.123 False 1.320 0.110
WRP WT 0.822 0.038 1.027 2.441 0.100 0.123 False 0.085 0.836
rapZE227Stop 0.130 -0.376 0.771 2.441 0.100 0.123 False 0.887 0.219
... ... ... ... ... ... ... ... ... ... ... ...
Lysine QC WT 0.076 0.175 1.129 7.393 0.002 0.005 True 1.121 0.104
rapZE227Stop 0.032 -0.359 0.779 7.393 0.002 0.005 True 1.490 0.083
WRP WT 0.622 -0.069 0.953 7.393 0.002 0.005 True 0.206 0.655
rapZE227Stop 0.004 -0.603 0.658 7.393 0.002 0.005 True 2.350 0.020
WT rapZE227Stop 0.004 -0.534 0.691 7.393 0.002 0.005 True 2.367 0.015

354 rows × 9 columns