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1.8k

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limma microarray block

updated 7 months ago by Gordon Smyth 50k • written 5.2 years ago by tleona3 • 0

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8.3k

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batch effect combat limma block

updated 8.6 years ago by Ryan C. Thompson ★ 7.9k • written 8.6 years ago by eleonoregravier ▴ 70

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3.1k

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limma covariate block paired samples technical replicates

updated 8.4 years ago by Aaron Lun ★ 28k • written 8.4 years ago by eleonoregravier ▴ 70

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5.5k

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limma microarray block paired linear model

9.4 years ago vas ▴ 40

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990

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diffbind block regression deseq2 chipseq

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

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2.0k

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limma sva block

updated 2.1 years ago by stuartthafass • 0 • written 9.5 years ago by kodream ▴ 20

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1.8k

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limma block design and contrast matrix

8.8 years ago choofd • 0

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1.3k

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limma roast mroast block

updated 7.8 years ago by Ryan C. Thompson ★ 7.9k • written 7.8 years ago by barbara.shih • 0

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2.7k

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batch effect Coeficents non estimable block random effects limma design matrix

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by mheydarpour ▴ 10

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1.5k

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deseq2 block pca

7.8 years ago akp • 0

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1.3k

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missmethyl diffvar design matrix limma block

updated 5.9 years ago by lhuang7 ▴ 50 • written 6.8 years ago by Simone ▴ 180

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1.3k

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time course block batch effect WGCNA

updated 7.1 years ago by Michael Love 41k • written 7.1 years ago by xie186 • 0

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936

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limma BatchEffect duplicatecorrelation block batch

updated 3.4 years ago by Kevin Blighe ★ 3.9k • written 3.4 years ago by Katherine • 0

13 results • Page 1 of 1

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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…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! I'll review my code from top to bottom.

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

Scholar to Michael Love 41k

Scholar to James W. MacDonald 65k

Supporter to JKim • 0