Bioconductor Batch Effect Correction

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921

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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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894

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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 6.3 years ago by Stephen Piccolo ▴ 600 • written 6.3 years ago by y.li.1 • 0

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1.8k

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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

7.3 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: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k

I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…

Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k

The behavior you have documented in not surprising and is explained in the featureCounts documentation. The first thing to understand is t…

Answer: Feature Counts -R XS Read Assignment Tag by Gordon Smyth 52k

No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…

Comment: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k

Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …

Comment: DESeq2 - Comparing Comparisons by James W. MacDonald 67k

Full disclosure: I don't use `DESeq2`, and find the contrasts specification confusing. Because of that, I generally recommend using `result…

Votes

Answer: Mapping Between GenBank ID's and Uniprot

Comment: What type of counts data to import for performing Isoform analysis in edgeR

A: Relations used in GO.db GOBPANCESTOR

Relations used in GO.db GOBPANCESTOR

Answer: RSubread output significantly different from bash Subread output

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