Showing : combat • reset
1
vote
2
replies
468
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
8 months ago takemoto • 0
0
votes
1
reply
276
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 9 months ago by 47k • written 9 months ago by • 0
1
vote
4
replies
2.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
16 months ago NewBioInfo ▴ 10
4
votes
6
replies
722
views
Combat and dds Object
DESeq2 combat
updated 7 days ago by ★ 2.0k • written 18 months ago by ▴ 20
0
votes
0
replies
356
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
22 months ago joannew • 0
1
vote
3
replies
696
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 22 months ago by 3.7k • written 22 months ago by • 0
1
vote
8
replies
839
views
Error in running Combat function
sva ComBat
updated 2.0 years ago by 3.7k • written 2.0 years ago by ▴ 10
0
votes
5
replies
543
views
Variable of interest in combat correction
sva combat
updated 2.2 years ago by 62k • written 2.2 years ago by ▴ 10
0
votes
3
replies
514
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 2.3 years ago by 3.7k • written 2.3 years ago by • 0
7
votes
6
replies
748
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 2.7 years ago by ▴ 840 • written 2.7 years ago by ▴ 10
1
vote
2
replies
491
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
0
votes
0
replies
1.1k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.1 years ago anne.bozack • 0
0
votes
1
reply
522
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 3.1 years ago by 3.7k • written 3.1 years ago by • 0
0
votes
1
reply
489
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 3.1 years ago by ▴ 840 • written 3.1 years ago by ▴ 10
0
votes
3
replies
558
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
8
votes
18
replies
8.2k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 23 months ago by • 0 • written 3.3 years ago by ▴ 10
2
votes
2
replies
774
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 3.3 years ago by 39k • written 3.3 years ago by ▴ 10
2
votes
3
replies
576
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by ▴ 50
0
votes
2
replies
625
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 3.4 years ago by 39k • written 3.4 years ago by • 0
0
votes
0
replies
446
views
The correct specification of the model matrix to ComBat
ComBat sva
3.5 years ago Sam ▴ 10
0
votes
6
replies
1.2k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 3.5 years ago by ▴ 260 • written 3.5 years ago by ▴ 660
7
votes
4
replies
2.8k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 3.5 years ago by 47k • written 3.5 years ago by ▴ 660
4
votes
16
replies
2.1k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 3.6 years ago by 39k • written 3.6 years ago by ▴ 10
3
votes
12
replies
1.9k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 3.8 years ago by 62k • written 3.8 years ago by ▴ 10
0
votes
0
replies
510
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 4.3 years ago by 47k • written 4.3 years ago by • 0
0
votes
2
replies
928
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
0
votes
0
replies
564
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
4.4 years ago jmsendoya • 0
0
votes
1
reply
1.2k
views
A problem in using Combat
sva combat
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by • 0
1
vote
1
reply
1.7k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 5.0 years ago by 47k • written 7.9 years ago by ▴ 130
1
vote
9
replies
1.6k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
5.0 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.6k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 5.1 years ago by • 0 • written 7.5 years ago by • 0
0
votes
0
replies
688
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
5.3 years ago Eddie Imada • 0
0
votes
1
reply
723
views
Combat prior plots good enough?
combat combat sva
5.3 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.7k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 5.3 years ago by ▴ 840 • written 5.3 years ago by • 0
2
votes
5
replies
4.1k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 5.5 years ago by 62k • written 5.5 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
5.5 years ago DataFanatic ▴ 10
0
votes
4
replies
1.7k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 5.7 years ago by 39k • written 5.7 years ago by • 0
0
votes
0
replies
946
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
5.7 years ago svlachavas ▴ 800
1
vote
1
reply
725
views
How to interpret the SVA results
SVA combat RNA-seq
updated 5.8 years ago by 62k • written 5.8 years ago by • 0
10
votes
4
replies
2.1k
views
Adjust for multiple batches using combat
combat sva limma
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
3
votes
4
replies
2.1k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 5.9 years ago by 39k • written 5.9 years ago by ▴ 10
0
votes
0
replies
803
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
6.0 years ago Ryan C. Thompson 7.8k
0
votes
6
replies
1.2k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
6.3 years ago User34591 • 0
5
votes
2
replies
6.3k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 30
5
votes
3
replies
3.1k
views
about SVA: matrix of corrected expression values
SVA COMBAT
6.3 years ago Bogdan ▴ 660
3
votes
8
replies
1.6k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 6.4 years ago by ▴ 30 • written 6.4 years ago by • 0
13
votes
2
replies
2.5k
views
voom with combat
limma voom combat batch effect
updated 6.5 years ago by 47k • written 6.5 years ago by ▴ 10
0
votes
1
reply
844
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 6.5 years ago by ▴ 400 • written 6.6 years ago by ▴ 800
50
votes
20
replies
35k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 6.7 years ago by • 0 • written 7.1 years ago by ▴ 110
50 results • Page 1 of 1
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Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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