Bioconductor MiRNAseq

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miRNAseq TCGAbiolinks TCGAAnalyze_DEA

3.0 years ago Gandino • 0

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deseq2 miRNASeq designmatrix Batch

updated 4.7 years ago by Michael Love 43k • written 4.7 years ago by anshulmbi • 0

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limma edger voom rnaseq mirnaseq

4.8 years ago atakanekiz ▴ 30

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deseq2 normalization miRNASeq

updated 5.2 years ago by Michael Love 43k • written 5.2 years ago by anshulmbi • 0

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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

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

Hi, what's the output from `dim(spe)`?

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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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