I'm trying to create a volcano plots using metabolomics data. Pvalues were obtained using scipy.stats ranksums function. It appears pvalues are repeated or rounded. My dataframe contains lo2fc values and I'm trying to add pvalues calculated in this way:
from scipy.stats import ranksums
groupA = subset_filter.iloc[:,4:7].values
groupB = subset_filter.iloc[:,7:10].values
# #Wilcoxon test using ranksums function
test = ranksums(groupA1,groupB2, axis=1)
Which is suppose to calculate over all rows (12k+) on those groups. Even though values are different it's giving me repeated pvalue values.