Bioconductor PlotMA

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plotMA ggplot2 plotPCA DESeq2

updated 7 months ago by Michael Love 41k • written 7 months ago by sara.jacobson • 0

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621

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matrixsubset DESeq2 plotMA

updated 3.0 years ago by Michael Love 41k • written 3.0 years ago by l.troxler ▴ 10

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889

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deseq2 plotMA rnaseq community analysis asymmetry

updated 4.2 years ago by Michael Love 41k • written 4.2 years ago by chaco001 • 0

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961

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agilent single channel plotMA background correction

updated 5.9 years ago by Gordon Smyth 50k • written 5.9 years ago by CantExitVIM ▴ 10

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1.1k

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deseq2 plotMA rnaseq logfoldchange

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by ap_vc21 • 0

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2.6k

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deseq2 plotma

6.6 years ago Yvan Wenger ▴ 50

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rstudio r plotMA

6.9 years ago g.k • 0

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4.8k

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deseq2 rnaseq plotMA deseq rna-seq

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by sjs0282 • 0

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3.7k

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limma plotMA

updated 8.7 years ago by Gordon Smyth 50k • written 8.7 years ago by Lisa Cohen ▴ 50

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2.4k

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normalization deseq2 plotMA meanSDplot

8.7 years ago aravenscraft • 0

10 results • Page 1 of 1

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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Votes

Answer: DEseq2 coefficient

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

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Scholar to Rory Stark ★ 5.2k

Popular Question to tangming2005 ▴ 190