Bioconductor Random effects

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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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997

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limma rna-seq edger random effects

updated 4.4 years ago by Gordon Smyth 50k • written 4.4 years ago by mjgarcia • 0

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1.2k

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random effects interaction limma rna-seq

5.0 years ago flippy23 • 0

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888

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rnaseq limma edger deseq2 random effects

5.3 years ago tcalvo ▴ 90

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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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2.8k

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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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1.2k

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deseq2 random effects batch effects RNA-seq rna-seq

updated 6.8 years ago by Michael Love 42k • written 6.8 years ago by Dipro • 0

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3.5k

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rna-seq edger mixed model random effects lme4

updated 7.9 years ago by Gordon Smyth 50k • written 7.9 years ago by Ekarl2 ▴ 80

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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

That ll be helpful. Thank you.

Comment: Log-cpm values from limma by Shaimaa Gamal • 0

I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…

Comment: DSS CpG coverage threshold by j.gilbert • 0

Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k

Segmentation is of the whole genome, I'll write some code for doing this later today.

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k

I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …

Votes

A: Volcanoplot with limma - RAW P-values or Adj.P-Values

Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

Answer: minfi latest update for EPIC V2 chip

A: Error in DESeqDataSet : some values in assay are not integers

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