‼️Why do we say that #methodsmatter?
Here’s a telling example.
Two very recent studies asked the exact same cancer #immunotherapy prediction question, on the exact same dataset.
They reached contradictory conclusions.
Why?
Slight changes in the #Bioinformatics methods used👇 twitter.com/NCIEytanRuppin/status/1610202233521438721
The changes are:
1.analyze data per cancer type vs. pan-cancer
2.use cutoff of 0.2 vs. 0.1 for calling a copy number alteration
The contradictory conclusions are:
1.aneuploidy score (AS) is not predictive of immunotherapy response
2.a new metric is predictive & outperforms AS
Here’s links to the two studies, Spurr et al was published in November 2022 & Cheng et al was posted on biorxiv in December 2022
nature.com/articles/s41588-022-01235-4
biorxiv.org/content/10.1101/2022.12.28.522101v1
This example is conceptually representative for some of the core principles that define #Bioinformatics #DataScience.
Minor changes in methods or statistical frameworks used can qualitatively change entire narratives.
Choice of thresholds is important
Reproducibility matters‼️