Bioconductor Synergy

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deseq2 contrast synergy

updated 4.0 years ago by Michael Love 40k • written 4.0 years ago by steven wink ▴ 90

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conditions design DESeq2 Synergy

updated 17 months ago by Michael Love 40k • written 17 months ago by johannesdolberg • 0

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synergy DESeq2 RNA-seq contrast

22 months ago • updated 21 months ago slcno • 0

3 results • Page 1 of 1

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Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k

You should use `removeBatchEffect` for that.

Comment: Interpret plot from DiffBind by Chris • 0

Thank you for the explanation! The purple (**gain**) in the control in the right bottom corner but on the y axis is labeled **loss** which …

Comment: Use with_go along with other filters in getBM function by RuBBiT0 ▴ 10

Thank you! I think that makes much sense to me.

Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k

Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …

Comment: Interpret plot from DiffBind by Chris • 0

Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?

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Answer: NA transcript values in my Txdb

Comment: Interpret plot from DiffBind

Answer: Use with_go along with other filters in getBM function

Answer: Interpret plot from DiffBind

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