Showing : lfc • reset
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7
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LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 6.9 years ago by • 0
1
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1
reply
1.3k
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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1
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1.8k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
4.6 years ago ayy2110 • 0
0
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6
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2.5k
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large range of LFC in DESeq2
deseq2 lfc betaprior
updated 3.2 years ago by 43k • written 7.1 years ago by • 0
17
votes
7
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16k
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DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 10
6
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4
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3.6k
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Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
8.6 years ago rkp • 0
4
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14
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22k
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standard error value (lfcSE) returned by DeSeq2
deseq2 deseq lfc lfcse standard error
updated 8.8 years ago by • 0 • written 8.9 years ago by • 0
2
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1
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3.1k
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Using Limma to identify any differences between multiple treatment groups (without making pairwise comparisons)
microarray limma multiple treatments lfc
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
8 results • Page 1 of 1
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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…
Votes
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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