Bioconductor Batch effect correction

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924

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batch effect limma batch effect correction

updated 5.8 years ago by Gordon Smyth 52k • written 5.8 years ago by ginlucks • 0

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899

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pvca batch effect batch effect correction

6.1 years ago Sebastian Hesse ▴ 70

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1.2k

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batch effect correction sva proteomics

6.1 years ago Sebastian Hesse ▴ 70

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1.5k

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deseq2 interactions batch effect correction grouping variable

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by mat.lesche ▴ 110

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2.4k

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scan.upc upc normalization batch effect correction

updated 6.4 years ago by Stephen Piccolo ▴ 600 • written 6.4 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 6.5 years ago by Gordon Smyth 52k • written 6.5 years ago by abelsousa • 0

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3.6k

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DESeq2 sva svaseq batch effect correction

6.9 years ago L_K • 0

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1.4k

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sva svaseq batch effect batch effects batch effect correction

7.4 years ago vedran.franke • 0

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1.2k

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limma voom Batch Effect Correction

updated 7.7 years ago by Aaron Lun ★ 28k • written 7.7 years ago by Dario Strbenac ★ 1.5k

9 results • Page 1 of 1

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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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