Bioconductor Batch effect correction

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945

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batch effect limma batch effect correction

updated 5.9 years ago by Gordon Smyth 52k • written 5.9 years ago by ginlucks • 0

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920

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pvca batch effect batch effect correction

6.2 years ago Sebastian Hesse ▴ 70

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1.3k

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batch effect correction sva proteomics

6.2 years ago Sebastian Hesse ▴ 70

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1.5k

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deseq2 interactions batch effect correction grouping variable

updated 6.3 years ago by Michael Love 43k • written 6.3 years ago by mat.lesche ▴ 110

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2.5k

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scan.upc upc normalization batch effect correction

updated 6.5 years ago by Stephen Piccolo ▴ 600 • written 6.5 years ago by y.li.1 • 0

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1.9k

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Limma differential gene expression batch effect correction covariates

updated 6.6 years ago by Gordon Smyth 52k • written 6.6 years ago by abelsousa • 0

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3.7k

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DESeq2 sva svaseq batch effect correction

7.0 years ago L_K • 0

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1.4k

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sva svaseq batch effect batch effects batch effect correction

7.5 years ago vedran.franke • 0

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1.2k

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limma voom Batch Effect Correction

updated 7.8 years ago by Aaron Lun ★ 28k • written 7.8 years ago by Dario Strbenac ★ 1.5k

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Comment: Identifying potentially associated gene set to drug response using GSVA by kl2023gege • 0

Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…

Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Votes

Answer: Unable to install nloptr

Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Selection of correct coefficients or contrasts in DESeq2

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Popular Question to bastien_chassagnol • 0