Bioconductor Blocking

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1.2k

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voom blocking limma

updated 22 months ago by Gordon Smyth 52k • written 22 months ago by Gerhard Thallinger ▴ 180

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1.0k

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edgeR blocking

updated 4.3 years ago by Yunshun Chen ▴ 900 • written 4.3 years ago by Molly • 0

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1.3k

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diffbind blocking model

updated 4.8 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by melnuesch ▴ 10

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1.9k

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edger limma paired blocking ruvseq

updated 5.3 years ago by Gordon Smyth 52k • written 5.3 years ago by ScA • 0

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3.3k

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limma repeated measurements blocking random effects

updated 5.5 years ago by Gordon Smyth 52k • written 5.5 years ago by Jane ▴ 10

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4.5k

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limma edger blocking paired samples

updated 6.8 years ago by Gordon Smyth 52k • written 6.8 years ago by anou ▴ 10

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1.1k

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diffbind differential binding analysis blocking

updated 7.6 years ago by Rory Stark ★ 5.2k • written 7.7 years ago by zhangly811 • 0

7 results • Page 1 of 1

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

Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do. I would personally check to see if there is any…

Comment: Can NanoString data be analyzed using DESeq2? by James W. MacDonald 68k

You can always discard, although you can also retain them to check for unexpected differences.

Comment: DESeq2 on NanoString Data by Michael Love 43k

Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc. It is close to SVA, we discuss both in the workflow…

Comment: DESeq2 on NanoString Data by thkapell ▴ 10

Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…

Comment: Can NanoString data be analyzed using DESeq2? by thkapell ▴ 10

Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…

Votes

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

Can NanoString data be analyzed using DESeq2?

Comment: Are voomByGroup and voomLmFit compatible?

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