Bioconductor Plotmds

Showing : plotmds • reset

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1.4k

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plotMDS limma

19 months ago Cen • 0

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4.0k

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plotMDS limma

updated 20 months ago by Gordon Smyth 52k • written 20 months ago by liujy4 • 0

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1.7k

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plotMDS PCA RNASeq MDS

updated 2.9 years ago by Gordon Smyth 52k • written 3.0 years ago by Raito92 ▴ 60

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1.6k

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limma plotMDS

3.6 years ago jamie.gearing ▴ 60

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4.8k

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edgeR plotmds differential gene expression MDS mdsplot

updated 6.2 years ago by Gordon Smyth 52k • written 6.2 years ago by ilovesuperheroes1993 • 0

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917

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plotMDS Cell lines limma

updated 6.5 years ago by Gordon Smyth 52k • written 6.5 years ago by Alexander Azarian ▴ 30

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1.1k

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tree bootstrap dgelist plotmds

7.0 years ago Larry K. • 0

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6.8k

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limma edger plotmds tmm masigpro

7.2 years ago dacaba.92 ▴ 10

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1.9k

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edger plotmds

7.4 years ago fawazfebin ▴ 60

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2.3k

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edger plotmds

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by mictadlo ▴ 10

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1.9k

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affymetrix microarrays sva combat sva batch effect plotMDS

updated 8.5 years ago by Jeff Leek ▴ 650 • written 8.5 years ago by svlachavas ▴ 840

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1.3k

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rgl plot3d plotmds

8.9 years ago Adam • 0

12 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

A: What is the "linear model" part used for in Limma?

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

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