Bioconductor Confounding factors

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differential gene expression nanostring confounding factors

updated 6.1 years ago by James W. MacDonald 67k • written 6.1 years ago by Guillaume Robert • 0

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limma design matrix paired samples confounding factors

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by yuabrahamliu • 0

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Comment: Are unequal sample sizes in differential gene expression (DGE) analysis a proble by Amora • 0

Both edgeR and DESeq2 can handle unequal group sizes if you ensure proper quality control and variance estimation. [sprunki retake][1] …

Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0

You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org

Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…

Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750

Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10

Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…

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Answer: EdgeR Biological CVs

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