Bioconductor Peaks

Showing : peaks • reset

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596

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ATACSeq peaks ATAC ChIPpeakAnno

9 months ago Raghad • 0

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1.0k

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Peaks MAC2 DiffBind

3.6 years ago Yuan Tian ▴ 290

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1.2k

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nucleosome peaks error Job

updated 5.2 years ago by James W. MacDonald 68k • written 5.2 years ago by anne.kannengiesser • 0

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diffbind chipseq counts peaks bedtools

updated 3.8 years ago by Rory Stark ★ 5.2k • written 6.9 years ago by Ni-Ar ▴ 10

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4.8k

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diffbind chipseq peaks dba is.na

6.9 years ago maria.kondili ▴ 10

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1.6k

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bioconductor annotation peaks

updated 7.3 years ago by Sean Davis 21k • written 7.3 years ago by schaud24 ▴ 10

6 results • Page 1 of 1

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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

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…

Votes

Comment: Use of limma R package with targeted proteomics for DE analysis

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

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