Bioconductor RNAseq analysis

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deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.2 years ago by Gavin Kelly ▴ 690 • written 7.2 years ago by c.nicole ▴ 50

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rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.6 years ago by Wolfgang Huber ★ 13k • written 6.6 years ago by svlachavas ▴ 840

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limma differential gene expression rnaseq analysis alignment RSEM

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.0 years ago by goldberg.jm ▴ 10

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rnaseq analysis

updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by marak • 0

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filterByExpression edgeR RNAseq analysis edger

updated 4.7 years ago by Gordon Smyth 52k • written 4.7 years ago by hcnbox • 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

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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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