Bioconductor Batch Correction

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975

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scrna-seq integration batch correction

updated 3.4 years ago by Aaron Lun ★ 28k • written 3.4 years ago by p.joshi ▴ 40

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611

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methylation ComBat Linear models batch correction AIC

updated 3.5 years ago by Kevin Blighe 3.8k • written 3.5 years ago by lucasmiranda42 • 0

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399

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DESeq2 batch correction

updated 3.5 years ago by James W. MacDonald 62k • written 3.5 years ago by MT ▴ 10

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599

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Diffbind ATAC batch correction blocking factor

updated 3.8 years ago by Rory Stark ★ 4.8k • written 3.8 years ago by rm1238 • 0

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685

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deseq2 differential expression batch correction design

updated 3.9 years ago by Michael Love 40k • written 4.0 years ago by wunderl ▴ 40

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910

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deseq2 differential expression batch correction

updated 4.0 years ago by Michael Love 40k • written 4.0 years ago by wunderl ▴ 40

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1.2k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 4.1 years ago by Vladimir Kiselev ▴ 150 • written 4.1 years ago by hamza_karakurt ▴ 50

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Comment: Extracting fitted expression matrix from Limma by sarah.kelliher • 0

Thank you Prof Smyth for your prompt and informative reply, much appreciated.

Answer: DESeq2 or edgeR for Presence and Absence of Proteins by ATpoint ★ 2.8k

No, both tools expect count data with certain distributional assumptions which are not satisfied by binary data. Since you're a master …

Comment: Visualization of negative log CPM values by Gordon Smyth 47k

Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…

Comment: Visualization of negative log CPM values by ATpoint ★ 2.8k

Applies to both.

Comment: Visualization of negative log CPM values by Sabiha ▴ 10

@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`

Votes

Answer: Extracting fitted expression matrix from Limma

Answer: DESeq2 or edgeR for Presence and Absence of Proteins

Comment: Visualization of negative log CPM values

Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?

Filtering low intensity probes in microarray data

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