Bioconductor Forum

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microbiome

updated 8 hours ago by Leo Lahti ▴ 40 • written 19 hours ago by Dario Strbenac ★ 1.5k

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107

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DESeq2 PCAtools

updated 15 hours ago by Michael Love 41k • written 2 days ago by Aaliya • 0

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105

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DESeq2 celda

updated 18 hours ago by Michael Love 41k • written 1 day ago by JalapenoCornbread • 0

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DiffBind

updated 18 hours ago by ATpoint ★ 4.0k • written 2 days ago by Shloka • 0

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RNAseq123

updated 22 hours ago by Gordon Smyth 50k • written 4 days ago by Lluís Revilla Sancho ▴ 730

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164

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EnhancedVolcano

1 day ago • updated 14 hours ago pl23 • 0

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258

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DESeq2

9 days ago • updated 16 hours ago ussarizona ▴ 10

7 results • Page 1 of 1

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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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