Bioconductor Combat SVA

Showing : Combat SVA • reset

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combat sva SVA sva ComBat batch effect

updated 8.0 years ago by W. Evan Johnson ▴ 850 • written 8.0 years ago by John Townsend ▴ 20

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svaseq combat sva RANseq batcheffect removebatcheffect

updated 7.5 years ago by Jakub ▴ 50 • written 7.5 years ago by amoltej ▴ 10

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combat sva batch effect comba

updated 7.5 years ago by Vegard Nygaard ▴ 110 • written 7.5 years ago by amoltej ▴ 10

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SVA combat sva batch effect

updated 7.7 years ago by Jeff Leek ▴ 650 • written 7.7 years ago by amoltej ▴ 10

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affymetrix microarrays sva combat sva batch effect plotMDS

updated 7.7 years ago by Jeff Leek ▴ 650 • written 7.7 years ago by svlachavas ▴ 830

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R Combat SVA

updated 8.3 years ago by Steve Lianoglou ★ 13k • written 8.3 years ago by nazaninhoseinkhan • 0

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combat sva input files

7.2 years ago arisarkar88 ▴ 40

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SVA combat sva leek

updated 2.9 years ago by chase.mateusiak • 0 • written 7.0 years ago by amoltej ▴ 10

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887

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combat sva sva

7.0 years ago alice.anlind • 0

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combat sva microarry Jeff leek

6.8 years ago DataFanatic ▴ 10

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combat combat sva

6.6 years ago Miss Agnieszka Aleksandra Golicz ▴ 40

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631

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combat sva

6.1 years ago jonellevillar • 0

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combat sva batch effect

5.9 years ago Fp • 0

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combat combat sva pamr limma design matrix sva

5.7 years ago jmsendoya • 0

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combat sva sga combat batch effect

8.0 years ago John Townsend ▴ 20

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ENmix combat.mc illumina450k combat sva

7.8 years ago DSP • 0

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927

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combat sva

7.7 years ago kkwon • 0

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954

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combat sva

7.4 years ago vinnu260 ▴ 10

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batch effect combat sva sva

7.2 years ago Ahdee ▴ 50

19 results • Page 1 of 1

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Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k

These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…

Answer: fgsea significant result by ATpoint ★ 4.1k

Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…

Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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