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software error Grange RangedData

4.7 years ago mawusse.agbessi • 0

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GenomicRanges GenomicFeatures grange distanceToNearest R

5.1 years ago rmash ▴ 20

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GRange

updated 6.0 years ago by James W. MacDonald 67k • written 6.0 years ago by Danny • 0

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R genomicranges granges grange

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Grange

10.0 years ago Bogdan ▴ 670

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Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…

Comment: makeContrastsDream for Interaction by abadgerw • 0

Thank you! I will try this out.

Comment: Merge Replicates vs Mixed Model by abadgerw • 0

Thanks, @gabrielhoffman The data is actually proteomics so it is intensity data which is why I did not use voom but rather ran ebayes wi…

Comment: ANOVA like approach of edgeR by Gordon Smyth 52k

To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …

Comment: DESeq2 sizefactors counfounded with biological treatment by Anna • 0

Hi James, Apologies (re: posting in the wrong place). Thank you so much for your response, that was exactly the help I needed. Best, A…

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Comment: makeContrastsDream for Interaction

Answer: Limma- Print-tip loess normalisation-printer layout information does not match M

Comment: Limma- Print-tip loess normalisation-printer layout information does not match M

Answer: ANOVA like approach of edgeR

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Popular Question to Marek Gierlinski ▴ 30

Scholar to Gordon Smyth 52k

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Popular Question to Hans-Ulrich Klein ▴ 330