Bioconductor MoleculeExperiment

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JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment

14 months ago Stefano Mangiola ▴ 40

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tidySpatialExperiment SpatialExperiment MoleculeExperiment

16 months ago info ▴ 10

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MoleculeExperiment DifferentialExpression DESeq2

updated 20 months ago by ATpoint ★ 4.9k • written 20 months ago by michelafrancesconi8 • 0

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MoleculeExperiment

updated 24 months ago by ATpoint ★ 4.9k • written 24 months ago by irenekokosaikia • 0

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Comment: ROAST compare results with complex design by Gordon Smyth 52k

It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.

Answer: ROAST compare results with complex design by James W. MacDonald 68k

You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Not sure I understand. You ask how to do something and then show how one would do so.

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Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi

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