Showing : rnaseqpower • reset
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA RNASeqPower DEGseq
written 14 months ago by • 0
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featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
15 months ago yasmin.hilliam ▴ 10
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
16 months ago sukeshinik5 ▴ 20
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.1 years ago drewhaydensteele • 0
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
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Typo in citation for RNASeqPower
RNASeqPower citation
3.6 years ago stephenjjohnson • 0
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How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 3.9 years ago by 53k • written 4.9 years ago by ▴ 60
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getting sample size for RNAseq experiment
rnaseqpower sspa sample size sequencing complex-design
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by • 0
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Depth or # of reads for RNASeqPower
rnaseqpower
11.2 years ago drnknmstrr • 0
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Power Calculation of multiple factors design of RNA-sequencing study
edgeR DESeq RNASeqPower edgeR DESeq RNASeqPower
11.9 years ago Guest User ★ 13k
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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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