Bioconductor Blocking

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replies

981

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voom blocking limma

updated 16 months ago by Gordon Smyth 52k • written 16 months ago by Gerhard Thallinger ▴ 180

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912

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edgeR blocking

updated 3.7 years ago by Yunshun Chen ▴ 900 • written 3.7 years ago by Molly • 0

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1.1k

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diffbind blocking model

updated 4.2 years ago by Rory Stark ★ 5.2k • written 5.3 years ago by melnuesch ▴ 10

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1.7k

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edger limma paired blocking ruvseq

updated 4.7 years ago by Gordon Smyth 52k • written 4.7 years ago by ScA • 0

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2.8k

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limma repeated measurements blocking random effects

updated 4.9 years ago by Gordon Smyth 52k • written 4.9 years ago by Jane ▴ 10

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4.1k

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limma edger blocking paired samples

updated 6.2 years ago by Gordon Smyth 52k • written 6.2 years ago by anou ▴ 10

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988

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diffbind differential binding analysis blocking

updated 7.0 years ago by Rory Stark ★ 5.2k • written 7.1 years ago by zhangly811 • 0

7 results • Page 1 of 1

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Comment: displaying the differential expression with deseq2 over 4X2 samples with the in by Martijn • 0

thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…

Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0

Thank you, this does clarify the available options.

Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k

If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…

Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0

Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…

Answer: Unused arguments error without used arguments in GSVA? by jodan • 0

It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…

Votes

Answer: Find exact GRanges match keeping metadata columns

Answer: Unused arguments error without used arguments in GSVA?

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