Bioconductor PlotMDS

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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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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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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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802

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plotMDS limma

9 months ago • updated 8 months ago Cen • 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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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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edger plotmds

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

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rgl plot3d plotmds

8.0 years ago Adam • 0

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924

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tree bootstrap dgelist plotmds

6.1 years ago Larry K. • 0

12 results • Page 1 of 1

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Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70

Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …

Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…

Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0

Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…

Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k

There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …

Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…

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A: Error in DESeqDataSet : some values in assay are not integers

Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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Popular Question to rohitsatyam102 ▴ 20