Bioconductor Blocking

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934

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voom blocking limma

updated 14 months ago by Gordon Smyth 52k • written 14 months ago by Gerhard Thallinger ▴ 180

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883

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edgeR blocking

updated 3.6 years ago by Yunshun Chen ▴ 900 • written 3.6 years ago by Molly • 0

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1.1k

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diffbind blocking model

updated 4.1 years ago by Rory Stark ★ 5.2k • written 5.1 years ago by melnuesch ▴ 10

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1.6k

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edger limma paired blocking ruvseq

updated 4.6 years ago by Gordon Smyth 52k • written 4.6 years ago by ScA • 0

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2.7k

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limma repeated measurements blocking random effects

updated 4.8 years ago by Gordon Smyth 52k • written 4.8 years ago by Jane ▴ 10

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4.0k

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limma edger blocking paired samples

updated 6.0 years ago by Gordon Smyth 52k • written 6.0 years ago by anou ▴ 10

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949

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diffbind differential binding analysis blocking

updated 6.9 years ago by Rory Stark ★ 5.2k • written 6.9 years ago by zhangly811 • 0

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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

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

Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…

Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k

Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …

Comment: fail to use addPerROIQC in Rmd by liu.n • 0

That's odd. So it can run successfully within markdown but would be failed when knitting?

Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0

> dim(spe) [1] 19962 425

Votes

Answer: contrast matrix design for a continuous variable

A: What's the difference between p.adjust and qvalue?

Answer: DESeq2- merging technical vs biological replicates

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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Popular Question to Ou, Jianhong ★ 1.3k