Showing : ComBat • reset
48
votes
20
replies
30k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 6.0 years ago by • 0 • written 6.4 years ago by ▴ 100
4
votes
21
replies
8.0k
views
DESeq2 and ComBat
deseq2 combat
updated 6.4 years ago by ▴ 600 • written 6.4 years ago by ▴ 100
8
votes
18
replies
6.7k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 15 months ago by • 0 • written 2.6 years ago by ▴ 10
6
votes
7
replies
6.4k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 6.6 years ago by 7.8k • written 6.6 years ago by ▴ 60
5
votes
2
replies
6.0k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by ▴ 30
1
vote
3
replies
5.6k
views
Combat - error - system is computationally singular
combat software error rnaseq complex-design
updated 7.6 years ago by ★ 2.6k • written 7.6 years ago by • 0
0
votes
4
replies
4.9k
views
ComBat: Error non-conformable arguments
ComBat
updated 7.1 years ago by 59k • written 7.1 years ago by • 0
0
votes
2
replies
4.2k
views
Combat in R (SVA package) error message
combat software error
updated 7.0 years ago by ★ 2.6k • written 7.0 years ago by • 0
0
votes
6
replies
4.1k
views
ComBat with multiple batches
sva combat 450k
6.4 years ago ben.run974 • 0
4
votes
4
replies
3.8k
views
sva::ComBat without covariate of interest?
sva combat
updated 7.5 years ago by ▴ 840 • written 7.5 years ago by ▴ 110
17
votes
18
replies
3.5k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 6.6 years ago by ▴ 840 • written 6.6 years ago by ▴ 780
1
vote
1
reply
3.5k
views
Combat generating negative values, should I log2 transform first?
combat batch effect
updated 6.6 years ago by ▴ 840 • written 6.6 years ago by ▴ 50
1
vote
5
replies
3.4k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 4.7 years ago by ★ 27k • written 4.7 years ago by ▴ 20
3
votes
4
replies
3.1k
views
Running Combat in SVA with NA values in matrix
sva combat
6.4 years ago CC ▴ 10
2
votes
6
replies
3.0k
views
Combat for batch effects
combat
7.2 years ago zhouxiuqing • 0
2
votes
2
replies
3.0k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 7.5 years ago by ▴ 840 • written 7.5 years ago by ▴ 10
0
votes
2
replies
2.9k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 6.3 years ago by 37k • written 6.3 years ago by • 0
10
votes
10
replies
2.9k
views
Method for batch correction
combat sva limma
updated 6.1 years ago by ▴ 110 • written 6.1 years ago by ▴ 50
1
vote
4
replies
2.8k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
6.9 years ago GFM ▴ 20
5
votes
3
replies
2.7k
views
about SVA: matrix of corrected expression values
SVA COMBAT
5.7 years ago Bogdan ▴ 640
5
votes
2
replies
2.5k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 7.5 years ago by ▴ 610 • written 7.5 years ago by ▴ 10
7
votes
3
replies
2.4k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 6.1 years ago by ▴ 840 • written 6.1 years ago by ▴ 20
7
votes
4
replies
2.4k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.8 years ago by 45k • written 2.8 years ago by ▴ 640
13
votes
2
replies
2.3k
views
voom with combat
limma voom combat batch effect
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 10
1
vote
1
reply
2.1k
views
sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 6.7 years ago by ▴ 610 • written 6.7 years ago by ▴ 10
0
votes
2
replies
2.0k
views
Remove batch effect - condition partially confounded by data
combat differential gene expression sva
updated 7.3 years ago by ▴ 610 • written 7.3 years ago by • 0
3
votes
4
replies
1.9k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 5.2 years ago by 37k • written 5.2 years ago by ▴ 10
10
votes
4
replies
1.8k
views
Adjust for multiple batches using combat
combat sva limma
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
1
vote
1
reply
1.6k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 4.3 years ago by 45k • written 7.2 years ago by ▴ 130
2
votes
7
replies
1.6k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
7.0 years ago edammer • 0
3
votes
12
replies
1.5k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 3.1 years ago by 59k • written 3.1 years ago by ▴ 10
0
votes
4
replies
1.5k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 5.0 years ago by 37k • written 5.0 years ago by • 0
0
votes
0
replies
1.5k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
6.3 years ago svlachavas ▴ 780
0
votes
8
replies
1.5k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 4.5 years ago by • 0 • written 6.8 years ago by • 0
3
votes
8
replies
1.4k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 5.7 years ago by ▴ 30 • written 5.7 years ago by • 0
2
votes
5
replies
1.4k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by • 0
1
vote
2
replies
1.4k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 6.3 years ago by ▴ 840 • written 6.3 years ago by ▴ 780
1
vote
9
replies
1.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
4.3 years ago jaro.slamecka ▴ 130
1
vote
1
reply
1.3k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 4.8 years ago by 59k • written 4.8 years ago by • 0
1
vote
2
replies
1.2k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat batch effect
7.2 years ago jaro.slamecka ▴ 130
4
votes
16
replies
1.2k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 3.0 years ago by 37k • written 3.0 years ago by ▴ 10
1
vote
1
reply
1.1k
views
ComBat (SVA) Application - Two Technical Effects
sva ComBat
updated 7.3 years ago by ▴ 600 • written 7.3 years ago by ▴ 360
0
votes
4
replies
1.1k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
8 months ago NewBioInfo • 0
0
votes
3
replies
1.0k
views
Problem in analysing microarray data with ComBat
combat
7.0 years ago melissa.sorci • 0
0
votes
4
replies
1000
views
Reproducibility of results with ComBat
sva combat
updated 6.7 years ago by ▴ 610 • written 6.7 years ago by • 0
0
votes
6
replies
992
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
5.6 years ago User34591 • 0
0
votes
6
replies
991
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by ▴ 640
0
votes
1
reply
984
views
A problem in using Combat
sva combat
updated 3.9 years ago by ▴ 840 • written 3.9 years ago by • 0
2
votes
3
replies
960
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 6.1 years ago by ▴ 400 • written 6.1 years ago by • 0
0
votes
0
replies
943
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
4.8 years ago DataFanatic • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30
Thanks, I'll trying playing a bit there. I have done some minor filtering already (requiring at least 5 counts in 10% of my samples, across…
Comment: ashr vs apeglm for interaction data by Michael Love 37k
I see why apeglm is conservative— the dispersion is very high within group. An idea would be to use ashr but do some additional filtering …
Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k
That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.
Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30
Hi Michael, Plots attached. Many of the large fold changes with `ashr` are driven by one sample per group, but a few are maybe a bit more …
Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10
Thanks! I have tried this; I am not sure after that how to find logeGFR associated probe? and also, how to filter significant probe? …
Votes
Comment: ashr vs apeglm for interaction data
Comment: How to figure out the FC value from Limma
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
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