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help DESeq2 DESeqDataSetFromMatrix rownames

updated 5 months ago by Kevin Blighe 3.4k • written 5 months ago by dorina.jamniczky • 0

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RNASeqData RNASeq GEO RNASeqR HELP

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help software error

updated 2.7 years ago by Martin Morgan 25k • written 2.7 years ago by mafusa20 • 0

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limma time series help

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clusterprofiler input files error help

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edger differential gene expression without replicate nested design help

updated 5.2 years ago by Aaron Lun ★ 27k • written 5.2 years ago by knipehf • 0

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R deseq2 differential gene expression help

5.3 years ago • updated 5.2 years ago fischer87 • 0

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limma help

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Comment: deseq2 machine sizing best practices for very large data set by aedavids • 0

Hi Michael These are bulk samples. I like your idea of running a couple of subsets to get a rough idea about the required resources. I am…

Comment: Error while running DE in DESeq2 by Michael • 0

Updating Deseq2 1.32.0 error was no longer an issue. May be an issue when using 1.30.1

Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k

Agree, noting just that "poscounts" is used quite a bit and fast (also it has been benchmarked in publications a few times). "iterate" is k…

Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset by josephbrown • 0

Regarding your "every gene contains at least one zero" error: I think when you run `vst()`, it will estimate size factors if they're not…

Comment: Combining two groups in contrast deseq2 by Michael Love 34k

I'd recommend you collaborate with a local statistician to help come up with an appropriate contrast for various hypotheses.

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Format roxgen comment (alternative to formatR)

Answer: Format roxgen comment (alternative to formatR)

How does DESeq2 handle zero counts in one condition?

The calculation of regularized logarithm

Answer: oligo package blas error

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