Bioconductor Volcanoplot

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RNA-seq DESeq2 volcanoplot

updated 11 months ago by Michael Love 43k • written 11 months ago by nramakr ▴ 10

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955

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DESeq2 volcanoplot LRT

updated 15 months ago by Michael Love 43k • written 15 months ago by Eric • 0

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2.6k

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DESeq2 volcanoplot deseq HELP contrast

updated 2.7 years ago by Basti ▴ 780 • written 2.7 years ago by Michael • 0

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1.6k

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plot volcano volcanoplot

updated 2.7 years ago by Basti ▴ 780 • written 2.7 years ago by Sooni ▴ 10

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969

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limma DEGreport Volcanoplot

updated 2.8 years ago by Gordon Smyth 53k • written 2.8 years ago by Mohammad • 0

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3.3k

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EnhancedVolcano RNASeqR R volcanoplot

updated 5.0 years ago by Kevin Blighe ★ 4.0k • written 5.0 years ago by camillab. ▴ 10

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limma volcanoplot pvalue logFC

updated 6.6 years ago by Gordon Smyth 53k • written 6.6 years ago by xingxd16 ▴ 20

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7.9k

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limma microarray volcanoplot color

updated 7.1 years ago by Gordon Smyth 53k • written 7.1 years ago by dmm204 • 0

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volcanoplot

updated 8.0 years ago by thokall ▴ 160 • written 8.0 years ago by Nithisha ▴ 10

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1.5k

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diffbind chipseq volcanoplot ggplot2

updated 8.1 years ago by Rory Stark ★ 5.2k • written 8.1 years ago by rbronste ▴ 60

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volcanoplot design and contrast matrix

updated 8.1 years ago by Gordon Smyth 53k • written 8.1 years ago by marongiu.luigi • 0

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13k

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volcanoplot limma fdr

8.3 years ago • updated 4.9 years ago tcalvo ▴ 100

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8.3k

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limma volcanoplot

updated 8.3 years ago by Gordon Smyth 53k • written 11.0 years ago by mccallionc403 • 0

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1.8k

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limma volcanoplot

updated 9.5 years ago by Aaron Lun ★ 29k • written 9.5 years ago by mheydarpour ▴ 10

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limma plot.MA volcanoplot oligo

updated 10.3 years ago by Gordon Smyth 53k • written 10.3 years ago by Gabriel Nathan Kaufman, Mr ▴ 60

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3.6k

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cummerbund ggplot2 size r volcanoplot

updated 10.9 years ago by James W. MacDonald 68k • written 10.9 years ago by ianmisner17 ▴ 20

16 results • Page 1 of 1

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Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

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Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

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