Bioconductor Nested

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415

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DESeq2 multifactorial nested

updated 13 months ago by Basti ▴ 780 • written 13 months ago by jd • 0

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1.0k

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nested DESeq2

updated 2.2 years ago by Michael Love 41k • written 2.3 years ago by yampolsk • 0

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1.0k

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deseq2 Phyloseq Nested

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by mpuli011 • 0

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760

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deseq2 Paired Nested

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by julia.chariker ▴ 10

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985

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deseq2 nested de

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by gaio.transposon • 0

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1.1k

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edgeR nested glm glmQLFit

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by jcalis ▴ 10

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2.5k

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edger nested design matrix differential expression

updated 9.2 years ago by Aaron Lun ★ 28k • written 9.2 years ago by Mauve • 0

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1.8k

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edger nested estimatedispersions

9.2 years ago Mauve • 0

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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…

Votes

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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