Bioconductor Random effects

Showing : random effects • reset

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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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982

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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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874

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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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2.7k

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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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1.2k

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deseq2 random effects batch effects RNA-seq rna-seq

updated 6.8 years ago by Michael Love 41k • 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 7.8 years ago by Gordon Smyth 50k • written 7.8 years ago by Ekarl2 ▴ 80

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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40

1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…

Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …

Answer: PCA plot suggestions by Michael Love 41k

For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…

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…

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Answer: Dominance Index for Shotgun Metagenomics Data

Answer: Math expression in shapeCustom legend in EnhancedVolcano

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)

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