Showing : ComBat • reset
4
votes
21
replies
11k
views
DESeq2 and ComBat
deseq2 combat
updated 8.3 years ago by ▴ 610 • written 8.3 years ago by ▴ 100
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 7.9 years ago by • 0 • written 8.3 years ago by ▴ 110
18
votes
18
replies
4.8k
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 8.5 years ago by ▴ 850 • written 8.5 years ago by ▴ 830
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.2 years ago by • 0 • written 4.5 years ago by ▴ 10
4
votes
16
replies
4.5k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 4.8 years ago by 41k • written 4.8 years ago by ▴ 10
3
votes
12
replies
3.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
10
votes
10
replies
3.9k
views
Method for batch correction
combat sva limma
updated 8.0 years ago by ▴ 110 • written 8.0 years ago by ▴ 60
1
vote
9
replies
2.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
6.2 years ago jaro.slamecka ▴ 140
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.2 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
5
votes
8
replies
2.3k
views
Combat and dds Object
DESeq2 combat
updated 14 months ago by ★ 4.0k • written 2.7 years ago by ▴ 40
0
votes
8
replies
2.3k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 6.4 years ago by • 0 • written 8.7 years ago by • 0
3
votes
8
replies
2.3k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 7.6 years ago by ▴ 30 • written 7.6 years ago by • 0
2
votes
7
replies
2.1k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
8.9 years ago edammer • 0
7
votes
7
replies
8.3k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 8.5 years ago by ★ 7.9k • written 8.5 years ago by ▴ 70
0
votes
6
replies
1.6k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
7.5 years ago User34591 • 0
0
votes
6
replies
5.9k
views
ComBat with multiple batches
sva combat 450k
8.3 years ago ben.run974 • 0
7
votes
6
replies
1.6k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 3.9 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
2
votes
6
replies
4.0k
views
Combat for batch effects
combat
9.1 years ago zhouxiuqing • 0
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 670
0
votes
6
replies
1.6k
views
Problem in analysing microarray data with ComBat
combat
updated 13 months ago by ▴ 850 • written 8.9 years ago by • 0
2
votes
5
replies
5.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
2
votes
5
replies
2.7k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 6.5 years ago by ▴ 850 • written 6.5 years ago by • 0
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva combat
updated 3.4 years ago by 65k • written 3.4 years ago by ▴ 10
10
votes
4
replies
2.9k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
1
vote
4
replies
5.7k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.6 years ago NewBioInfo ▴ 10
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
0
votes
4
replies
6.3k
views
ComBat: Error non-conformable arguments
ComBat
updated 9.0 years ago by 65k • written 9.0 years ago by • 0
1
vote
4
replies
3.5k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
8.8 years ago GFM ▴ 20
0
votes
4
replies
1.4k
views
Reproducibility of results with ComBat
sva combat
updated 8.6 years ago by ▴ 650 • written 8.6 years ago by • 0
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 670
3
votes
4
replies
4.4k
views
Running Combat in SVA with NA values in matrix
sva combat
8.3 years ago CC ▴ 10
0
votes
4
replies
375
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
14 days ago • updated 13 days ago Lucy ▴ 60
0
votes
4
replies
2.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
4
votes
4
replies
4.5k
views
sva::ComBat without covariate of interest?
sva combat
updated 9.4 years ago by ▴ 850 • written 9.4 years ago by ▴ 110
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.1 years ago by 41k • written 7.1 years ago by ▴ 10
2
votes
3
replies
1.0k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by ▴ 80
7
votes
3
replies
3.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 8.0 years ago by ▴ 850 • written 8.0 years ago by ▴ 20
2
votes
3
replies
1.4k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 8.0 years ago by ▴ 420 • written 8.0 years ago by • 0
5
votes
3
replies
3.8k
views
about SVA: matrix of corrected expression values
SVA COMBAT
7.6 years ago Bogdan ▴ 670
1
vote
3
replies
6.5k
views
Combat - error - system is computationally singular
combat software error rnaseq complex-design
updated 9.5 years ago by ★ 3.0k • written 9.5 years ago by ▴ 10
0
votes
3
replies
977
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
0
votes
3
replies
1.0k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.5 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
2
replies
3.4k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
5
votes
2
replies
7.1k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 7.5 years ago by ▴ 70 • written 7.5 years ago by ▴ 30
1
vote
2
replies
1.9k
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 8.2 years ago by ▴ 850 • written 8.2 years ago by ▴ 830
0
votes
2
replies
5.4k
views
Combat in R (SVA package) error message
combat software error
updated 8.9 years ago by ★ 3.0k • written 8.9 years ago by • 0
1
vote
2
replies
913
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
0
votes
2
replies
1.1k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
5
votes
2
replies
3.1k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 9.4 years ago by ▴ 650 • written 9.4 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
WEHI, Melbourne, Australia, just now
France, 3 minutes ago
France, 4 minutes ago
Pakistan, 5 minutes ago
Jerusalem, 11 minutes ago
Traffic: 814 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6