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Should I pre-normalize RNAseq data before combat?
R normalize combat rna-seq batch effect written 1 day ago by zhaoliang0302 • 0 • updated 1 day ago by Kevin Blighe ♦ 45k
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99
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Remove batch effect for many RNA-seq
sva combat rna-seq batch effect written 2 days ago by Shaway • 0
6
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165
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How to assess RNA-Seq batch correction success?
batch correction deseq2 combat limma rna-seq written 8 weeks ago by cancer_tantra • 10
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svaseq and combat
combat sva effect batch written 2.2 years ago by Folder40g • 120 • updated 4 months ago by liull_hust • 0
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398
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Batch correction: Before and After Visualisation
combat deseq2 svaseq rna-seq written 4 months ago by prabin.dm • 160
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1
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222
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1
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Multiplatform batch correction using combat
combat microarray written 4 months ago by Devyani • 30
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1
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11k
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1
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removing batch effects using ComBat and SVA
R sva combat batch effect written 3.1 years ago by LJ • 180 • updated 5 months ago by Agustin Gonzalez-Vicente • 40
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284
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sva combat removes wanted biological variation
R sva combat rna-seq pca written 5 months ago by exin • 50 • updated 5 months ago by zx8754 ♦ 7.8k
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287
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ComBat correction with one batch containing only one sample - keep or remove?
proteome sva combat R written 8 months ago by hesse.sebastian • 80 • updated 5 months ago by Biostar ♦♦ 20
1
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246
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Normalise batch effects for Percent Spliced In (PSI) matrice
sva combat splicing written 6 months ago by ZheFrench • 240
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1
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315
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1
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How to remove batch effect in copy number segment mean
cna segment combat batch effect written 8 months ago by sugus • 30 • updated 6 months ago by Biostar ♦♦ 20
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1
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1.1k
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1
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ComBat on TCGA RNAseq data generates all NAN
tcga combat written 2.1 years ago by mforde84 • 1.2k • updated 8 months ago by coyoung • 0
6
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1
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3.1k
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1
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Using ComBat on RNASeq FPKM counts
combat rna-seq written 2.7 years ago by ebrudermanver • 50 • updated 11 months ago by Kevin Blighe ♦ 45k
1
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1
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943
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Help with multiple batch effects
sva batch effects combat written 12 months ago by fp89 • 20 • updated 12 months ago by genomax ♦ 69k
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1
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523
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1
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Batch effect correction
sva combat matlab written 13 months ago by gstavropoulos1991 • 10
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593
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1
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Removing batch effects between Affymetrix and Agilent platforms using ComBat
agilent combat microarray affymetrix written 14 months ago by nazaninhoseinkhan • 360 • updated 14 months ago by andrew.j.skelton73 ♦ 5.8k
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1
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12 follow
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Batch effects : ComBat or removebatcheffects (limma package) ?
sva batch effects combat limma written 23 months ago by lessismore • 640 • updated 20 months ago by Kevin Blighe ♦ 45k
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4.9k
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Error in while (change > conv) { : missing value where TRUE/FALSE needed
combat rna-seq batch effect written 21 months ago by lessismore • 640 • updated 21 months ago by Biostar ♦♦ 20
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1
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1.7k
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6 follow
1
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RNA-Seq Batch correction negative values
batch-effect combat scran rna-seq sva written 21 months ago by rmf • 680 • updated 21 months ago by Kevin Blighe ♦ 45k
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6 follow
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SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva batch effects combat written 2.0 years ago by lessismore • 640 • updated 22 months ago by Biostar ♦♦ 20
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1
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1
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Time point microarray data correcting for batch effects
combat microarray batch effect written 23 months ago by tleona3 • 10 • updated 23 months ago by mforde84 • 1.2k
3
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1
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1.3k
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1
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Converting beta value to M value (when beta=1)
dna methylation combat written 2.0 years ago by janhuang.cn • 150 • updated 2.0 years ago by Devon Ryan ♦ 91k
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584
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meta-analysis: can I still combine the 2 studies?
microbiome 16s combat meta-analysis otu written 2.1 years ago by alowi33 • 0
3
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1.3k
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any recommended tools for batch effect and normalization not written in R?
python batch effect combat rna-seq R written 2.3 years ago by dyollluap • 300 • updated 2.2 years ago by Biostar ♦♦ 20
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1
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1.2k
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R: Error when using ComBat
R sva combat written 2.9 years ago by kkj3083 • 0 • updated 2.2 years ago by susanna.downing • 0
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569
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Scan Dates will not show
bioconductor affy combat written 2.3 years ago by jmannhei • 0
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Correcting batch effect from known variables in RnBeads using Combat
450k combat methylation rnbeads batch effect written 2.3 years ago by rahel14350 • 30
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Differential expression on Combat-adjusted FPKM
fpkm combat rna-seq differential expression written 2.6 years ago by mare116 • 0
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1
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Batch correction (mass spectrometry data)
biostatistics R sva combat batch correction written 2.6 years ago by mkhadka10 • 0
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4.9k
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3
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Remove Surrogate Variables and Batch
R sva combat written 4.6 years ago by tucanj • 80 • updated 2.8 years ago by ddiez • 1.8k
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