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limma fit design RNASeq edgeR

8 months ago Sabiha ▴ 20

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5

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rnaseq linear model fit deseq2

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by lina.faller ▴ 10

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dexseq fit matrix warning

updated 3.1 years ago by koushik • 0 • written 7.8 years ago by Assa Yeroslaviz ★ 1.5k

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limma goodness fit linear model

updated 9.9 years ago by Gordon Smyth 52k • written 9.9 years ago by nonCodingGene ▴ 10

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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

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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