Now published: Ten common mistakes that could ruin your enrichment analysis
Glad to share with you our published article Ten common mistakes that could ruin your enrichment analysis . The work was done by Anusuiya Bora (Burnet Bioinformatics, Deakin Uni), Matthew McKenzie (Deakin) and I. My working group got interested into pathway enrichment analysis in around 2020/2021 because I was receiving review requests for manuscripts and many of them suffered from severe problems, leading me to believe that these issues were prevalent. Our first article on this theme Wijesooriya et al, 2022 demonstrated that severe problems were really common across a big sample of peer-reviewed articles including: Lack of p-value correction. Wrong background list. Lack of methodological details. We showed that problems 1 and 2 led to dramatic biases in results that could alter the conclusions of transcriptome studies. Due to reviewer disagreements, we were unable to provide a more comprehensive set of best practices in that article, but this remained a priorit...
