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filter deseq2

updated 2.4 years ago by Michael Love 43k • written 2.4 years ago by PD • 0

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R filter limma Normalization Microarray

2.4 years ago Abdul ▴ 20

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filter gate_quad_tmix gt_gating

3.5 years ago • updated 3.4 years ago Pierre • 0

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flowCore openCyto Summary Result Filter

updated 5.3 years ago by Jake Wagner ▴ 310 • written 5.5 years ago by noviello • 0

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RNA WGCNA filter

6.2 years ago modarzi ▴ 10

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filter deseq2

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by charles.foster ▴ 180

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rtracklayer gff filter

updated 6.6 years ago by Michael Lawrence ★ 11k • written 6.6 years ago by alslonik • 0

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deseq2 filter genefilter

updated 7.8 years ago by Michael Love 43k • written 7.9 years ago by Björn • 0

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loop filter

written 7.8 years ago by kritikamish99 ▴ 10

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DGElist filter edgeR

updated 8.2 years ago by Gordon Smyth 53k • written 8.2 years ago by alakatos ▴ 130

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limma filter genelist differential gene expression

updated 8.9 years ago by Gordon Smyth 53k • written 8.9 years ago by bi_Scholar • 0

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missing data filter

updated 9.8 years ago by James W. MacDonald 68k • written 9.8 years ago by rgescudero • 0

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flowcore gate subsetting filter

updated 10.0 years ago by Jiang, Mike ★ 1.3k • written 10.0 years ago by peterfoster ▴ 20

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probe filter subset gene symbol affy

10.5 years ago alakatos ▴ 130

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bioconductor mas5 perfectmatch affymetrixchip filter

updated 10.5 years ago by James W. MacDonald 68k • written 10.6 years ago by svlachavas ▴ 840

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deseq filter reads

10.7 years ago • updated 10.6 years ago ccheung • 0

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variantannotation vcf fixed filter

10.7 years ago Anna N. • 0

17 results • Page 1 of 1

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

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