Bioconductor Limma-voom

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limma-voom design matrix limma time-course limma design matrix limma

6.1 years ago SPbeginner • 0

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2.6k

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edger limma-voom paired samples

7.6 years ago aec ▴ 90

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1.3k

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limma edger voom voomWithQualityWeights limma-voom

updated 6.4 years ago by Gordon Smyth 50k • written 6.4 years ago by Guido Hooiveld ★ 3.9k

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2.5k

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limma-voom duplicatecorrelation random effects

updated 5.5 years ago by Gordon Smyth 50k • written 5.5 years ago by tcalvo ▴ 90

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1.2k

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edger limma-voom voom

updated 7.2 years ago by Aaron Lun ★ 28k • written 7.2 years ago by gregory.l.stone ▴ 10

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1.8k

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rnaseq limma limma-voom Tutorial

updated 7.1 years ago by Aaron Lun ★ 28k • written 7.1 years ago by icxa0409 • 0

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3.0k

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limma limma-voom limma paired analysis limma contrast matrix

updated 7.1 years ago by Aaron Lun ★ 28k • written 7.1 years ago by gregory.l.stone ▴ 10

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4.7k

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voom limma-voom tximport edger

updated 7.1 years ago by Ryan C. Thompson ★ 7.9k • written 7.1 years ago by johnmcma ▴ 10

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2.5k

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limma-voom sva duplicatecorrelation

updated 6.8 years ago by sina.nassiri ▴ 130 • written 6.8 years ago by aec ▴ 90

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2.4k

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normalization sva limma-voom

updated 6.8 years ago by Gordon Smyth 50k • written 6.8 years ago by aec ▴ 90

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salmon tximport limma-voom

updated 6.6 years ago by Michael Love 41k • written 6.6 years ago by Sandip Darji ▴ 30

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1.7k

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limma-voom voom limma rna-seq

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by vd4mmind • 0

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1.1k

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limma-voom rnaseq normalization

6.3 years ago bilcodygm • 0

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1.2k

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limma limma-voom goseq

updated 6.2 years ago by Gordon Smyth 50k • written 6.2 years ago by joelrosa • 0

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4.1k

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voom limma-voom voomwithqualityweights rna-seq

updated 6.2 years ago by Matthew Ritchie ▴ 1000 • written 6.2 years ago by anne.biton ▴ 20

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1.2k

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quantile normalization limma-voom

updated 6.2 years ago by Gordon Smyth 50k • written 6.2 years ago by bilcodygm • 0

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1.8k

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limma limma-voom

updated 6.1 years ago by Gordon Smyth 50k • written 6.1 years ago by Peter Langfelder ★ 3.0k

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2.0k

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limma limma-voom

updated 12 months ago by blackdesgin • 0 • written 6.1 years ago by SPbeginner • 0

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1.7k

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limma limma-voom limma design matrix confounders

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 years ago by S.Bamopoulos ▴ 10

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1.8k

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rna-seq time series patient limma-voom

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by aec ▴ 90

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2.0k

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limma-voom deseq2 EdgeR

updated 5.5 years ago by Steve Lianoglou ★ 13k • written 5.5 years ago by Raymond ▴ 20

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1.5k

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deseq2 limma voom limma-voom rnaseq

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by bharata1803 ▴ 60

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889

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limma limma-voom StatisticalMethod

updated 15 months ago by Gordon Smyth 50k • written 15 months ago by jay • 0

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629

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limma-voom smooth-quantile-normalization quantro

21 months ago raf4 ▴ 20

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1.3k

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limma limma-voom rnaseq voom

updated 2.6 years ago by Gordon Smyth 50k • written 2.6 years ago by taur.vil • 0

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862

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limma limma-trend limma-voom

updated 3 months ago by floriandeckert ▴ 30 • written 17 months ago by hainct • 0

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940

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variancePa variancePartition limma-voom dream

updated 13 months ago by Gordon Smyth 50k • written 14 months ago by Le • 0

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1.4k

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limma-voom rnaseq differential gene expression

7.6 years ago Javier Gutierrez-Achury • 0

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1.7k

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limma limma design matrix limma contrast matrix limma paired analysis limma-voom

updated 7.2 years ago by Gordon Smyth 50k • written 7.2 years ago by gregory.l.stone ▴ 10

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1.7k

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limma limma-voom

updated 7.2 years ago by Aaron Lun ★ 28k • written 7.2 years ago by gregory.l.stone ▴ 10

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1.2k

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rnaseq edger limma-voom

updated 6.3 years ago by Michael Love 41k • written 6.3 years ago by bilcodygm • 0

31 results • Page 1 of 1

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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

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'…

Votes

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

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

Awards • All

Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

Supporter to JKim • 0