Bioconductor PlotMA

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plotMA ggplot2 plotPCA DESeq2

updated 6 months ago by Michael Love 41k • written 6 months ago by sara.jacobson • 0

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611

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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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873

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deseq2 plotMA rnaseq community analysis asymmetry

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by chaco001 • 0

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951

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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 6.1 years ago by Michael Love 41k • written 6.1 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

6.8 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 8.6 years ago by Gordon Smyth 50k • written 8.6 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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Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240

They are reorder in the decreasing order.

Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0

Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…

Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0

Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)

Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0

Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…

Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240

The genes are automatically ordered within `fgsea`, there is no need to sort them manually.

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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

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