Bioconductor RemoveBatchEffect

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13k

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limma removeBatchEffect heatmap clustering

updated 8.3 years ago by Bernd Klaus ▴ 610 • written 8.3 years ago by Ekarl2 ▴ 80

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10k

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limma differential gene expression clustering removebatcheffect

updated 6.6 years ago by Gordon Smyth 50k • written 6.6 years ago by lirongrossmann ▴ 80

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8.6k

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limma removebatcheffect

updated 6.6 years ago by Gordon Smyth 50k • written 9.7 years ago by Rao,Xiayu ▴ 550

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5.9k

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limma removebatcheffect deseq2

updated 7.9 years ago by Ryan C. Thompson ★ 7.9k • written 7.9 years ago by ompandey ▴ 10

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4.2k

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batch effect removebatcheffect edgeR rld DEseq2

5.7 years ago Antonio Ahn ▴ 10

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3.5k

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RUVSeq FPKM removeBatchEffect RNA-seq sva

updated 2.3 years ago by ATpoint ★ 4.0k • written 3.1 years ago by Xiaojie Cheng • 0

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2.6k

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ruvseq edger ruvg removebatcheffect

updated 8.2 years ago by Aaron Lun ★ 28k • written 8.2 years ago by g.atla ▴ 10

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2.6k

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edger removeBatchEffect cpm logCPM limma

4.9 years ago altintas.ali • 0

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2.3k

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sva R removebatcheffect

6.9 years ago aina.jene ▴ 10

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2.2k

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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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2.0k

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sva removebatcheffect R

updated 7.0 years ago by sina.nassiri ▴ 130 • written 7.0 years ago by aina.jene ▴ 10

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1.6k

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edger r batcheffect clustering removeBatchEffect

updated 5.0 years ago by James W. MacDonald 65k • written 5.0 years ago by Biologist ▴ 110

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1.5k

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SC3 batch effect removebatcheffect

updated 6.4 years ago by Vladimir Kiselev ▴ 150 • written 6.4 years ago by muad.abdelhay ▴ 10

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1.4k

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edgeR removeBatchEffect nested design

updated 7.5 years ago by Aaron Lun ★ 28k • written 7.5 years ago by Jenny Drnevich ★ 2.0k

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1.3k

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limma removebatcheffect

7.4 years ago Keifa ▴ 10

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916

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Microarray DifferentialExpression limma MicroarrayData removebatcheffect

15 months ago dqt • 0

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770

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removeBatchEffect limma

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by Sam ▴ 10

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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30

1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…

Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …

Answer: PCA plot suggestions by Michael Love 41k

For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

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Answer: Math expression in shapeCustom legend in EnhancedVolcano

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

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