Bioconductor Plotmds

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812

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plotMDS limma

9 months ago • updated 8 months ago Cen • 0

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1.8k

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plotMDS limma

updated 10 months ago by Gordon Smyth 50k • written 10 months ago by liujy4 • 0

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1.2k

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plotMDS PCA RNASeq MDS

updated 2.1 years ago by Gordon Smyth 50k • written 2.1 years ago by Raito92 ▴ 60

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1.2k

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limma plotMDS

2.7 years ago jamie.gearing ▴ 60

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3.8k

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edgeR plotmds differential gene expression MDS mdsplot

updated 5.3 years ago by Gordon Smyth 50k • written 5.3 years ago by ilovesuperheroes1993 • 0

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731

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plotMDS Cell lines limma

updated 5.6 years ago by Gordon Smyth 50k • written 5.6 years ago by Alexander Azarian ▴ 30

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924

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tree bootstrap dgelist plotmds

6.1 years ago Larry K. • 0

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5.8k

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limma edger plotmds tmm masigpro

6.4 years ago dacaba.92 ▴ 10

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1.5k

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edger plotmds

6.6 years ago fawazfebin ▴ 60

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2.0k

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edger plotmds

updated 6.6 years ago by Aaron Lun ★ 28k • written 6.6 years ago by mictadlo ▴ 10

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1.6k

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affymetrix microarrays sva combat sva batch effect plotMDS

updated 7.7 years ago by Jeff Leek ▴ 650 • written 7.7 years ago by svlachavas ▴ 830

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1.1k

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rgl plot3d plotmds

8.0 years ago Adam • 0

12 results • Page 1 of 1

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

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Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

A: Print Differentially Expressed Exons From Dexseq Results

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