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5.7 years ago dogancan • 0
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linear mixed models using edgeR+limma
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updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 10
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How to make PCA plot using DESeq2 for a group design
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how to analyze WGCNA results?
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
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edgeR + tximport: calcNormFactors and the usage of offsets
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updated 12 months ago by 53k • written 5.7 years ago by ▴ 20
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ATACSeqQC - error when splitting files using mm10
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DESeq2 LRT test for multi-factor designs
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Better way to find head to head GRanges?
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updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 180
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CAGEr quantilePositions() takes forever to run
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5.7 years ago mirkocelii ▴ 40
0
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950
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DESeq2 for normalizing metagenomic counts
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updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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plot function in flowType under R4.0.0
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5.7 years ago lifengt • 0
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How to find differential gene and expression analysis using DESeq or edgeR
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updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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updated 5.7 years ago by 25k • written 5.7 years ago by • 0
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updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
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How to overlap heatmaps on Gviz?
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5.7 years ago kris.petrini • 0
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Error while installing GSVA
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lfcShrink giving error
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error when forging a BSgenome
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updated 5.7 years ago by 4.3k • written 5.7 years ago by ▴ 10
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Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
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ChIPseeker error when I wnat to get tagMatrix
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5.7 years ago hfyuan2016 • 0
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tximport from RSEM expected counts: is it possible to import from a table rather than a file?
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updated 5.7 years ago by 68k • written 5.7 years ago by • 0
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RMarkdown in combination with OUTRIDER
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Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
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5.7 years ago AishaD • 0
1
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correct use of regularized log/VST values from deseq2
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5.7 years ago alexis.weinreb • 0
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5.7 years ago john.gordon.yellow • 0
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listSRAfile: Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
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5.7 years ago Aditya ▴ 160
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updated 5.7 years ago by 53k • written 5.7 years ago by • 0
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MakeOrgPackageFromNCBI SQL error
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updated 5.7 years ago by 68k • written 5.7 years ago by • 0
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Behaviour of getCTSS on a CAGEset - extra reads?
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updated 5.7 years ago by ▴ 180 • written 6.5 years ago by ▴ 20
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46,726 results • Page 166 of 935
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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