Bioconductor TCGAutils

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581

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TCGAutils

updated 6 weeks ago by James W. MacDonald 68k • written 6 weeks ago by xiaofeiwang18266 ▴ 50

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918

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normalization RNASEQ Normalization TCGAutils TCGA

updated 2.3 years ago by ATpoint ★ 4.7k • written 2.3 years ago by Deniz • 0

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2.2k

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MultiAssayExperiment curatedTCGAData TCGAutils

4.2 years ago svlachavas ▴ 840

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1.5k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.2 years ago by Marcel Ramos 700 • written 4.2 years ago by svlachavas ▴ 840

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1.6k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.2 years ago by Marcel Ramos 700 • written 4.4 years ago by svlachavas ▴ 840

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4.9k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 5.6 years ago by Marcel Ramos 700 • written 5.6 years ago by Dario Strbenac ★ 1.6k

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928

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TCGAutils

updated 5.9 years ago by Levi Waldron ★ 1.1k • written 5.9 years ago by vittorio.fortino • 0

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1.7k

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TCGAutils multiassayexperiment coad

updated 6.7 years ago by Marcel Ramos 700 • written 6.7 years ago by mario.zanfardino ▴ 160

8 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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