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TCGA GenomicDataCommons

11 weeks ago Ezgi ▴ 30

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GenomicDataCommons R

updated 16 months ago by Kevin Blighe 3.1k • written 16 months ago by gv ▴ 40

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 23 months ago by Marcel Ramos 540 • written 23 months ago by Dario Strbenac ★ 1.5k

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genomicdatacommons tcga gdc rest http

updated 2.4 years ago by Sean Davis 21k • written 2.4 years ago by mk ▴ 20

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Comment: DESeq2: Variable Importance by lolol • 0

Ah yes, I see the deviance now in mcols. Would I use this to calculate the pseudo R-squared (McFaddens), comparing each model with a single…

Answer: How to do annotation with Limma by Guido Hooiveld ★ 3.0k

For the HTA2.0 arrays should not use `hgu95av2.db`, which is the annotation library for the, ehh, human U95 set of Affymetrix arrays! You s…

Comment: DESeq2: Variable Importance by Michael Love 33k

Yes, `deviance` is an output in the `mcols`, so you could rotate through variables, excluding them in the LRT. Or you could use the other p…

Answer: Hard coding in DiffBind DBA.R line 968 by Rory Stark ★ 3.9k

Thank you for noticing and reporting this potential issue relating to the minimum number of sample replicates required to form a contrast. …

Comment: DESeq2: Variable Importance by lolol • 0

When you say observing the deviance, you mean utilizing the likelihood ratio test with the reduced model (exclude the last variable). Am I …

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Answer: How to do annotation with Limma

Final List of Deprecated Packages for Bioc3.13

Answer: RNAseq : identical sample-sample distances after using limma::removeBatchEffect

Comment: Use of arrayWeights with two treatment groups

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Popular Question to Guido Hooiveld ★ 3.0k