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MouseGastrulationData Normalization BatchEffect

updated 5 months ago by Jonathan Griffiths ▴ 30 • written 5 months ago by xyang2 ▴ 120

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SingleR MouseGastrulationData

updated 13 months ago by Aaron Lun ★ 26k • written 14 months ago by jma1991 ▴ 60

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Answer: DiffBind by Rory Stark ★ 3.8k

I'll answer the second question first. You should not accessing the `$binding` matrix directly -- the chromosome names are factor numbers,…

Comment: How to download the ChAMP dependency ChAMPdata by shepherl 2.6k

You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…

Comment: DiffBind reporting error by Rory Stark ★ 3.8k

If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…

Comment: limma - removing samples? by RMP87 • 0

Thank you very much for the explanation. Making it more precise. Could I analyze and normalize all samples from a dataset even though I had…

Comment: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ? by Saulius • 0

Yes - I think you are right once more. Thanks for taking so much time to look into this. Size factors come in twice in the code of `cqn`: …

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Effect of feature number on adjusted p-values

A: Using DADA2 output for DESeq2

Comment: Error wth Installation BiocManager

Answer: limma - removing samples?

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