First of all I apologize without the question is very basic, I am taking my first steps in bioinformatics.
We are evaluating the correlation (using the Pearson, Kendall or Spearman method) between gene expression and miRNA expression using the corAndPvalue function of WCGNA.
The resulting structure would be a DataFrame containing all combinations between each gene with each miRNAs, containing the following columns:
Gene miRNA Correlation P-value Gen_1 miRNA_1 0,959 0.00311 Gen_1 miRNA_2 -0,039 0.1041 Gen_1 miRNA_3 -0,344 0.0021 Gen_2 miRNA_1 0,1333 0.00451 Gen_2 miRNA_2 0,877 0.07311 ...
Considering the huge number of correlation tests we are going to evaluate, we need to adjust the p-values to avoid correlations due to chance. Bonferroni does not seem to be the best solution, so we would use Benjamini-Hochberg method (BH). The question is:
The BH correction for the
miRNA_1 combination, should consider the p-values of all combinations that include Gen_1 (Option 1), or should consider all the p-values of all the genes x miRNA combinations (Option 2)?
For example, let’s assume an expression dataset of 20,000 genes and another of 15,000 miRNAs
miRNA_1 we would use 15,000 p-values (
miRNA_1 we would use 300,000,000 p-values (
miRNA_15000 and so on).
Documentation of the method fdrcorrection from Python Statsmodels library suggests that for negative correlations (that could be frequent in a mRNA x miRNA correlation analysis) Benjamini-Yekutieli would work better; is that right? Or Benjamini-Hochberg method would be appropiated for this case?
Any kind of help would be much appreciated, thanks in advance!
I made the same question in CrossValidated forum and got an excellent answer!
The important part:
You need to correct for all of the comparisons you are doing. So if that's 300,000,000 comparisons you need to correct for that many multiple comparisons.
For more information check the answer in the link above
Answered by Genarito on November 15, 2021
1 Asked on November 5, 2020 by fullmooninu
1 Asked on November 5, 2020 by daro-rocha
0 Asked on October 18, 2020 by ibio_rep1
1 Asked on October 17, 2020
0 Asked on October 9, 2020 by dale-handley
1 Asked on September 27, 2020 by abiologist
1 Asked on September 10, 2020 by hepcat72
4 Asked on September 1, 2020 by rob-john
2 Asked on August 31, 2020
0 Asked on August 30, 2020 by annabelperry
7 Asked on August 19, 2020 by user3138373
0 Asked on August 11, 2020 by mmphysics
2 Asked on August 8, 2020 by justine-vandendorpe
2 Asked on August 5, 2020
Get help from others!