Bioconductor Knitr

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votes

1.2k

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RStudio MOFA2 bug knitr

updated 2.3 years ago by James W. MacDonald 68k • written 2.4 years ago by Kevin Coombes ▴ 430

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replies

1.1k

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knitr boxplot

updated 5.1 years ago by James W. MacDonald 68k • written 5.1 years ago by poojitha.stemcell ▴ 10

vote

1.3k

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rmarkdown knitr

updated 6.1 years ago by Aaron Lun ★ 28k • written 6.1 years ago by Keith Hughitt ▴ 180

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16k

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rmarkdown rstudio knitr

8.4 years ago Jon Bråte ▴ 260

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2.1k

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software error knitr

updated 8.7 years ago by Martin Morgan 25k • written 8.7 years ago by idomtamir ▴ 10

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1.5k

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knitr vignettes built bioccheck no-ASCII

8.9 years ago kmezhoud ▴ 10

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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