Bioconductor Confounding

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edger confounding

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by Victoria • 0

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limma batch effect design matrix microarray confounding

7.7 years ago svlachavas ▴ 840

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limma voom continuous interactions confounding

8.3 years ago lanhuong ▴ 20

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limma gene expression confounding adjustment paired

9.2 years ago Loodramon • 0

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limma GSA confounding within-pair analysis 450k

9.8 years ago Aileen Bahl ▴ 10

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Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0

It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!

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: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

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