Showing : combat • reset
0
votes
0
replies
128
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
4 months ago joannew • 0
0
votes
3
replies
222
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 4 months ago by 3.2k • written 4 months ago by • 0
1
vote
8
replies
341
views
Error in running Combat function
sva ComBat
updated 6 months ago by 3.2k • written 6 months ago by ▴ 10
0
votes
5
replies
189
views
Variable of interest in combat correction
sva combat
updated 8 months ago by 57k • written 8 months ago by ▴ 10
0
votes
3
replies
218
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 10 months ago by 3.2k • written 10 months ago by • 0
7
votes
6
replies
263
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 14 months ago by ▴ 840 • written 15 months ago by ▴ 10
1
vote
2
replies
180
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
0
replies
434
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
19 months ago anne.bozack • 0
0
votes
1
reply
161
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 19 months ago by 3.2k • written 20 months ago by • 0
0
votes
1
reply
220
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 20 months ago by ▴ 840 • written 20 months ago by ▴ 10
0
votes
3
replies
250
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 21 months ago by 25k • written 21 months ago by • 0
4
votes
18
replies
4.0k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 5 months ago by • 0 • written 22 months ago by • 0
2
votes
2
replies
311
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 22 months ago by 33k • written 22 months ago by ▴ 10
2
votes
3
replies
310
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 23 months ago by ▴ 800 • written 23 months ago by ▴ 50
0
votes
2
replies
230
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 23 months ago by 33k • written 23 months ago by • 0
0
votes
0
replies
258
views
The correct specification of the model matrix to ComBat
ComBat sva
23 months ago Sam ▴ 10
0
votes
6
replies
754
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 23 months ago by ▴ 260 • written 24 months ago by ▴ 620
7
votes
4
replies
1.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 620
4
votes
16
replies
451
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 2.1 years ago by 33k • written 2.1 years ago by ▴ 10
3
votes
12
replies
1.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 10
0
votes
0
replies
335
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
2
replies
608
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
0
votes
0
replies
343
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
2.9 years ago jmsendoya • 0
0
votes
1
reply
638
views
A problem in using Combat
sva combat
updated 3.1 years ago by ▴ 840 • written 3.1 years ago by • 0
1
vote
1
reply
1.5k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 3.5 years ago by 43k • written 6.4 years ago by ▴ 130
1
vote
9
replies
1.1k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
3.5 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.2k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 3.6 years ago by • 0 • written 6.0 years ago by • 0
0
votes
0
replies
508
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
3.8 years ago Eddie Imada • 0
0
votes
1
reply
492
views
Combat prior plots good enough?
combat combat sva
3.8 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.1k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 3.8 years ago by ▴ 840 • written 3.8 years ago by • 0
1
vote
5
replies
2.6k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 4.0 years ago by 57k • written 4.0 years ago by • 0
0
votes
0
replies
846
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
4.0 years ago DataFanatic • 0
0
votes
4
replies
1.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 4.2 years ago by 33k • written 4.2 years ago by • 0
0
votes
0
replies
696
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
4.2 years ago svlachavas ▴ 780
1
vote
1
reply
540
views
How to interpret the SVA results
SVA combat RNA-seq
updated 4.3 years ago by 57k • written 4.3 years ago by • 0
10
votes
4
replies
1.5k
views
Adjust for multiple batches using combat
combat sva limma
updated 4.4 years ago by ★ 27k • written 4.4 years ago by • 0
3
votes
4
replies
1.5k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 4.4 years ago by 33k • written 4.4 years ago by ▴ 10
0
votes
0
replies
564
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
4.5 years ago Ryan C. Thompson 7.6k
0
votes
6
replies
771
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
4.8 years ago User34591 • 0
4
votes
2
replies
5.6k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 4.8 years ago by ▴ 60 • written 4.8 years ago by ▴ 20
5
votes
3
replies
2.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
4.8 years ago Bogdan ▴ 620
3
votes
8
replies
1.2k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 4.9 years ago by ▴ 30 • written 4.9 years ago by • 0
13
votes
2
replies
2.1k
views
voom with combat
limma voom combat batch effect
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
0
votes
1
reply
600
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 5.1 years ago by ▴ 390 • written 5.1 years ago by ▴ 780
44
votes
20
replies
26k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.2 years ago by • 0 • written 5.6 years ago by ▴ 100
2
votes
3
replies
814
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 5.2 years ago by ▴ 390 • written 5.3 years ago by • 0
0
votes
0
replies
603
views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
5.3 years ago John Townsend ▴ 20
7
votes
3
replies
2.2k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 5.3 years ago by ▴ 840 • written 5.3 years ago by ▴ 20
10
votes
10
replies
2.5k
views
Method for batch correction
combat sva limma
updated 5.3 years ago by ▴ 110 • written 5.3 years ago by ▴ 50
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