2/2 Using BH/Bonferroni often leaves proteomics (Olink) results underpowered in my analysis, even when scRNA-seq produces plenty of DEGs.
Findings (my interpretation): qvalue and permFDP provide higher sensitivity with only a marginal hit to specificity.
Findings (my interpretation): qvalue and permFDP provide higher sensitivity with only a marginal hit to specificity.
January 4, 2026 at 1:52 PM
2/2 Using BH/Bonferroni often leaves proteomics (Olink) results underpowered in my analysis, even when scRNA-seq produces plenty of DEGs.
Findings (my interpretation): qvalue and permFDP provide higher sensitivity with only a marginal hit to specificity.
Findings (my interpretation): qvalue and permFDP provide higher sensitivity with only a marginal hit to specificity.
@tommytang.bsky.social I think you should add permFDP pubmed.ncbi.nlm.nih.gov/36693222/ . I found it very useful in my analysis. I recently tried to make the package more robust github.com/mihem/permFD...
GitHub - mihem/permFDP at gh_actions
An R package for correcting p-values for multiple hypothesis testing in comparative quantitative omics experiments using permutation-based FDP estimation. - GitHub - mihem/permFDP at gh_actions
github.com
January 3, 2026 at 9:59 PM
@tommytang.bsky.social I think you should add permFDP pubmed.ncbi.nlm.nih.gov/36693222/ . I found it very useful in my analysis. I recently tried to make the package more robust github.com/mihem/permFD...
@tommytang.bsky.social it works for me on my PC but not on my smartphone.
January 1, 2026 at 7:50 PM
@tommytang.bsky.social it works for me on my PC but not on my smartphone.
@tommytang.bsky.social nice. However if I change to R , loading the R environment crashes chatomics-labs.base44.app/TutorialView... SE for other tutorials
Chatomics Labs
chatomics-labs.base44.app
December 30, 2025 at 8:02 PM
@tommytang.bsky.social nice. However if I change to R , loading the R environment crashes chatomics-labs.base44.app/TutorialView... SE for other tutorials
Nice video, and wow you build that fast.
We usually write a manuscript with Google Docs, so we can even work in parallel, I can use citation manager in there etc. What advantage does korppi offer?
We usually write a manuscript with Google Docs, so we can even work in parallel, I can use citation manager in there etc. What advantage does korppi offer?
December 19, 2025 at 2:20 PM
Nice video, and wow you build that fast.
We usually write a manuscript with Google Docs, so we can even work in parallel, I can use citation manager in there etc. What advantage does korppi offer?
We usually write a manuscript with Google Docs, so we can even work in parallel, I can use citation manager in there etc. What advantage does korppi offer?
And what's your opinion on vs code with R vs positron? Tried positron a year and missed a few things including copilot and remote ssh, which is now available. But not sure it is as good.
October 24, 2025 at 10:08 AM
And what's your opinion on vs code with R vs positron? Tried positron a year and missed a few things including copilot and remote ssh, which is now available. But not sure it is as good.
Or maybe just vs code with r extension, Claude sonnet agent with GitHub copilot . Works great for me.
October 22, 2025 at 4:36 PM
Or maybe just vs code with r extension, Claude sonnet agent with GitHub copilot . Works great for me.