Bioconductor Blocking

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replies

692

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voom blocking limma

updated 6 months ago by Gordon Smyth 50k • written 6 months ago by Gerhard Thallinger ▴ 180

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694

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edgeR blocking

updated 3.0 years ago by Yunshun Chen ▴ 840 • written 3.0 years ago by Molly • 0

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1.4k

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edger limma paired blocking ruvseq

updated 4.0 years ago by Gordon Smyth 50k • written 4.0 years ago by ScA • 0

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1.9k

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limma repeated measurements blocking random effects

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by Jane ▴ 10

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923

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diffbind blocking model

updated 3.5 years ago by Rory Stark ★ 5.2k • written 4.5 years ago by melnuesch ▴ 10

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3.6k

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limma edger blocking paired samples

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by anou ▴ 10

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806

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diffbind differential binding analysis blocking

updated 6.3 years ago by Rory Stark ★ 5.2k • written 6.3 years ago by zhangly811 • 0

7 results • Page 1 of 1

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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k

Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…

Votes

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

Answer: Cross-species analysis - how to compute the mid parent value?

Awards • All

Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

Supporter to JKim • 0