Why do all the pvalue and qvalue are same?

[StanfordShuyuShi]

Hi! I run DISCOVER (Python version) in PyCharm (Python 3.9.13), but I got the same pvalue and qvalue. input:

import numpy as np import pandas as pd import discover import discover.datasets data = pd.read_excel(r'my sample.xlsx', index_col=0) print(data.iloc[:5, :5]) events = discover.DiscoverMatrix(data) subset = data.sum(1) > 5 result_data = discover.pairwise_discover_test(events[subset]) print(result_data) print(result_data.significant_pairs().iloc[:4, :4])

output:

number of pairs tested: 903 proportion of true null hypotheses: 1.0 number of significant pairs at a maximum FDR of 0.01: 178

              gene1                gene2    pvalue    qvalue

0 Human herpesvirus 6B Human adenovirus C 0.001003 0.005207 1 Human herpesvirus 6B Human herpesvirus 7 0.001003 0.005207 2 Human herpesvirus 6B Human adenovirus E 0.001003 0.005207 3 Human herpesvirus 6B Human herpesvirus 8 0.001003 0.005207

Dose anybody can help you? I'd appreciate your help a lot!

[scanisius]

Without seeing the data that you use, it is difficult to pinpoint the source of your problem. Are all p-values the same or just the top ones that you are showing here?