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6
votes
2
answers
173
views
5 follow
2
answers
Normalization and batch effects correction in RNA-Seq data
combat rna-seq written 6 weeks ago by elb • 190 • updated 6 weeks ago by rpolicastro • 1.9k
5
votes
2
answers
214
views
5 follow
2
answers
How to perform batch correction when we have only single condition?
batcheffects sva deseq2 combat written 12 weeks ago by svp • 240
12
votes
2
answers
16k
views
2
answers
removing batch effects using ComBat and SVA
R sva combat batch effect written 4.4 years ago by LJ • 230 • updated 3 months ago by zhao03 • 30
0
votes
0
answers
220
views
0
answers
Batch effect for SNP array
sva combat snp batch effect written 8 months ago by Taylor95 • 10 • updated 7 months ago by Biostar ♦♦ 20
0
votes
0
answers
271
views
0
answers
Extra adjustment variables during batch effect correction
combat rna-seq batch effect correction written 9 months ago by mike-zx • 210
3
votes
1
answer
256
views
1
answer
Can I use batch effect correction "by parts"?
combat rna-seq batch effect written 9 months ago by mike-zx • 210
4
votes
1
answer
735
views
1
answer
sva combat removes wanted biological variation
R sva combat rna-seq pca written 20 months ago by exin • 50 • updated 11 months ago by Biostar ♦♦ 20
0
votes
0
answers
210
views
0
answers
In SVA, the percent of biological variable of interest didnot change after adding SV1.
R sva combat written 11 months ago by dhwani2410 • 0 • updated 11 months ago by Kevin Blighe ♦ 66k
12
votes
1
answer
1.9k
views
7 follow
1
answer
Batch correction in DESeq2
deseq2 combat batch effect written 12 months ago by Arindam Ghosh • 310 • updated 12 months ago by Kevin Blighe ♦ 66k
3
votes
1
answer
294
views
1
answer
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
sva batch effects combat rna-seq cross-species written 13 months ago by rodguinea • 0 • updated 13 months ago by i.sudbery ♦ 9.4k
3
votes
1
answer
1.0k
views
1
answer
analysis of multiple batches and multiple treatment conditions in scRNA-seq
scrna-seq deseq2 combat limma edger written 14 months ago by Bogdan • 1.0k • updated 14 months ago by sofiagreen72211 • 30
0
votes
1
answer
934
views
1
answer
Should I pre-normalize RNAseq data before combat?
R normalize combat rna-seq batch effect written 15 months ago by zhaoliang0302 • 10 • updated 15 months ago by Kevin Blighe ♦ 66k
2
votes
1
answer
602
views
1
answer
Remove batch effect for many RNA-seq
sva combat rna-seq batch effect written 15 months ago by Shaway • 0
6
votes
1
answer
489
views
1
answer
How to assess RNA-Seq batch correction success?
batch correction deseq2 combat limma rna-seq written 17 months ago by borkk • 90
0
votes
0
answers
2.8k
views
0
answers
svaseq and combat
combat sva effect batch written 3.4 years ago by Folder40g • 140 • updated 19 months ago by liull_hust • 0
0
votes
0
answers
1.9k
views
0
answers
Batch correction: Before and After Visualisation
combat deseq2 svaseq rna-seq written 19 months ago by prabin.dm • 190
3
votes
1
answer
451
views
1
answer
Multiplatform batch correction using combat
combat microarray written 20 months ago by Devyani • 30
0
votes
0
answers
738
views
0
answers
ComBat correction with one batch containing only one sample - keep or remove?
proteome sva combat R written 23 months ago by Sebastian Hesse • 180 • updated 21 months ago by Biostar ♦♦ 20
1
vote
0
answers
572
views
0
answers
Normalise batch effects for Percent Spliced In (PSI) matrice
sva combat splicing written 21 months ago by ZheFrench • 300
0
votes
1
answer
1.1k
views
1
answer
How to remove batch effect in copy number segment mean
cna segment combat batch effect written 23 months ago by sugus • 50 • updated 22 months ago by Biostar ♦♦ 20
0
votes
1
answer
1.6k
views
1
answer
ComBat on TCGA RNAseq data generates all NAN
tcga combat written 3.3 years ago by mforde84 • 1.3k • updated 23 months ago by coyoung • 0
6
votes
1
answer
4.7k
views
1
answer
Using ComBat on RNASeq FPKM counts
combat rna-seq written 4.0 years ago by ebrudermanver • 80 • updated 2.2 years ago by Kevin Blighe ♦ 66k
1
vote
1
answer
2.3k
views
1
answer
Help with multiple batch effects
sva batch effects combat written 2.3 years ago by fp89 • 20 • updated 2.3 years ago by genomax ♦ 91k
1
vote
1
answer
914
views
1
answer
Batch effect correction
sva combat matlab written 2.4 years ago by gstavropoulos1991 • 10
0
votes
1
answer
1.2k
views
1
answer
Removing batch effects between Affymetrix and Agilent platforms using ComBat
agilent combat microarray affymetrix written 2.5 years ago by nazaninhoseinkhan • 410 • updated 2.5 years ago by andrew.j.skelton73 ♦ 6.0k
22
votes
1
answer
18k
views
17 follow
1
answer
Batch effects : ComBat or removebatcheffects (limma package) ?
sva batch effects combat limma written 3.2 years ago by lessismore • 930 • updated 3.0 years ago by Kevin Blighe ♦ 66k
12
votes
0
answers
8.7k
views
8 follow
0
answers
Error in while (change > conv) { : missing value where TRUE/FALSE needed
combat rna-seq batch effect written 3.0 years ago by lessismore • 930 • updated 3.0 years ago by Biostar ♦♦ 20
7
votes
1
answer
2.9k
views
6 follow
1
answer
RNA-Seq Batch correction negative values
batch-effect combat scran rna-seq sva written 3.1 years ago by rmf • 970 • updated 3.1 years ago by Kevin Blighe ♦ 66k
12
votes
0
answers
5.2k
views
7 follow
0
answers
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva batch effects combat written 3.3 years ago by lessismore • 930 • updated 3.1 years ago by Biostar ♦♦ 20
2
votes
1
answer
1.1k
views
1
answer
Time point microarray data correcting for batch effects
combat microarray batch effect written 3.2 years ago by tleona3 • 10 • updated 3.2 years ago by mforde84 • 1.3k
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