Bioconductor RNASeq

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BatchQC BatchEffect RNASeq

updated 40 minutes ago by James W. MacDonald 65k • written 9 hours ago by ttt • 0

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RNASeq scRNAseq

1 day ago Bibi • 0

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1.9k

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sgseq rnaseq

updated 4 days ago by Leonard Goldstein ▴ 220 • written 6.7 years ago by Sylvain Foisy ▴ 80

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256

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DifferentialExpression TimeCourse timeOmics edgeR RNAseq

updated 5 days ago by Gordon Smyth 50k • written 6 days ago by Ashley • 0

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228

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DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq

updated 18 days ago by ATpoint ★ 4.1k • written 18 days ago by james.zhang20 • 0

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166

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DESeq2 RNAseq

updated 25 days ago by Michael Love 42k • written 25 days ago by kcarey • 0

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192

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limma RNASeq voom

written 27 days ago by taur.vil • 0

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245

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technicalReplicates BatchEffect limma RNASeq

4 weeks ago • updated 28 days ago catv • 0

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317

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limma edgeR RNASeq

updated 10 days ago by Gordon Smyth 50k • written 4 weeks ago by Shaimaa Gamal • 0

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892

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clusterProfiler RNASeq

updated 26 days ago by Guangchuang Yu ★ 1.2k • written 14 months ago by ruiqi.li ▴ 10

10 results • Page 1 of 1

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Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k

Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …

Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k

It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.

Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k

Since batch is orthogonal to the treatment, you just add a batch factor to your model.

Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0

Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…

Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k

edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…

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Answer: Subsetting RNAseq data | voomaByGroup()

biomaRt not working - lazy table error

Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it

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