Bioconductor TCGAWorkflow

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TCGAWorkflow

10 months ago sameerahmadguru • 0

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TCGAWorkflow

20 months ago Begin-R • 0

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TCGAWorkflow

updated 2.3 years ago by ATpoint ★ 4.6k • written 2.3 years ago by fatemehfakhari74 • 0

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TCGAbiolinks TCGAWorkflow

2.3 years ago hemangininaik09 • 0

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DifferentialExpression TCGAWorkflow

3.1 years ago Sam ▴ 10

5 results • Page 1 of 1

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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k

Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…

Votes

Answer: nightmare to make custom txdb for genomes from ToxoDB

Comment: nightmare to make custom txdb for genomes from ToxoDB

Answer: Normalizing batch effects using technical replicates for DGE analysis between tw

Answer: nightmare to make custom txdb for genomes from ToxoDB

A: Advice on correcting for batch effect using DESeq2

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Popular Question to Jenny Drnevich ★ 2.0k

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Scholar to James W. MacDonald 67k