Bioconductor Limma

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limma

written 8 weeks ago by A.Barden ▴ 20

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DESeq2 RNASeq edgeR limma

9 days ago • updated 8 days ago Mariami • 0

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416

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limpa ProteomicsWorkflow limma

6 weeks ago • updated 28 days ago Andrew Pattison • 0

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1.7k

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CAMERA limma

updated 14 days ago by Gordon Smyth 53k • written 18 months ago by Jiahao Tian • 0

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limma

updated 2 hours ago by Robert Castelo ★ 3.4k • written 17 hours ago by A.Barden ▴ 20

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Comment: Can sample-level weights be used when analysing GSVA scores in limma? by Robert Castelo ★ 3.4k

Hi Gordon, thanks for giving your advice on how to use sample weights with GSVA scores. I have not used so far sample weights with GSVA sco…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

It looks to me that everything is working ok and limpa has done the right thing. You data has a lot of missing values, with the proportion …

Answer: Can sample-level weights be used when analysing GSVA scores in limma? by Gordon Smyth 53k

Yes, you could probably use the voom sample weights for an analysis of the GSVA scores for the same data, although I have never tried it. …

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 160

You are correct. Thank you for noticing some of this 'pollution' with "_2" suffixes was unnecessary. I posted an updated SILVA classifier …

Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0

Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.

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A: The meaning of results produced by the bamQC function implemented in the ATACseq

The meaning of results produced by the bamQC function implemented in the ATACseqQC

A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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