Showing : Combat • reset
5
votes
2
replies
286
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
9 weeks ago Federico ▴ 10
0
votes
0
replies
312
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
8 months ago Jitendra ▴ 10
1
vote
2
replies
1.2k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
18 months ago takemoto • 0
0
votes
1
reply
683
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 19 months ago by 48k • written 19 months ago by • 0
1
vote
4
replies
4.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.2 years ago NewBioInfo ▴ 10
5
votes
8
replies
1.9k
views
Combat and dds Object
DESeq2 combat
updated 10 months ago by ★ 3.6k • written 2.3 years ago by ▴ 20
0
votes
0
replies
570
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
2.7 years ago joannew • 0
1
vote
4
replies
1.5k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 weeks ago by • 0 • written 2.7 years ago by • 0
1
vote
8
replies
1.2k
views
Error in running Combat function
sva ComBat
updated 2.9 years ago by 3.9k • written 2.9 years ago by ▴ 10
0
votes
5
replies
873
views
Variable of interest in combat correction
sva combat
updated 3.1 years ago by 64k • written 3.1 years ago by ▴ 10
0
votes
3
replies
876
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.2 years ago by 3.9k • written 3.2 years ago by • 0
7
votes
6
replies
1.4k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 3.6 years ago by ▴ 850 • written 3.6 years ago by ▴ 10
1
vote
2
replies
792
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 3.9 years ago by 48k • written 3.9 years ago by • 0
0
votes
0
replies
1.7k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.9 years ago anne.bozack • 0
0
votes
1
reply
790
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 4.0 years ago by 3.9k • written 4.0 years ago by • 0
0
votes
1
reply
744
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 4.0 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
0
votes
3
replies
859
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
8
votes
18
replies
11k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 2.8 years ago by • 0 • written 4.2 years ago by ▴ 10
2
votes
2
replies
1.1k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 4.2 years ago by 41k • written 4.2 years ago by ▴ 10
2
votes
3
replies
909
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 80
0
votes
2
replies
993
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
0
votes
0
replies
692
views
The correct specification of the model matrix to ComBat
ComBat sva
4.3 years ago Sam ▴ 10
0
votes
6
replies
1.6k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 670
7
votes
4
replies
3.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 670
4
votes
16
replies
3.7k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 10
3
votes
12
replies
2.8k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 4.6 years ago by 64k • written 4.6 years ago by ▴ 10
0
votes
0
replies
707
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 5.2 years ago by 48k • written 5.2 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
0
replies
802
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
5.2 years ago jmsendoya • 0
0
votes
1
reply
1.6k
views
A problem in using Combat
sva combat
updated 5.4 years ago by ▴ 850 • written 5.4 years ago by • 0
1
vote
1
reply
1.9k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 5.8 years ago by 48k • written 8.7 years ago by ▴ 140
1
vote
9
replies
2.2k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
5.8 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.1k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 6.0 years ago by • 0 • written 8.3 years ago by • 0
0
votes
0
replies
931
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
6.1 years ago Eddie Imada • 0
0
votes
1
reply
987
views
Combat prior plots good enough?
combat combat sva
6.2 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
2.3k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 6.2 years ago by ▴ 850 • written 6.2 years ago by • 0
2
votes
5
replies
5.2k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 6.3 years ago by 64k • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
6.3 years ago DataFanatic ▴ 10
0
votes
4
replies
2.1k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
0
votes
0
replies
1.2k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
6.6 years ago svlachavas ▴ 820
1
vote
1
reply
949
views
How to interpret the SVA results
SVA combat RNA-seq
updated 6.7 years ago by 64k • written 6.7 years ago by • 0
10
votes
4
replies
2.6k
views
Adjust for multiple batches using combat
combat sva limma
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
3
votes
4
replies
2.6k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
0
votes
0
replies
1.0k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
6.8 years ago Ryan C. Thompson 7.8k
0
votes
6
replies
1.5k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
7.1 years ago User34591 • 0
5
votes
2
replies
6.9k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 7.1 years ago by ▴ 70 • written 7.1 years ago by ▴ 30
5
votes
3
replies
3.6k
views
about SVA: matrix of corrected expression values
SVA COMBAT
7.2 years ago Bogdan ▴ 670
3
votes
8
replies
2.1k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 7.2 years ago by ▴ 30 • written 7.2 years ago by • 0
13
votes
2
replies
2.9k
views
voom with combat
limma voom combat batch effect
updated 7.4 years ago by 48k • written 7.4 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: RNASeq time course analysis, missing time points for control by Gordon Smyth 48k
You could fit a spline trend with design matrix `treatment+spline`. Then it won't matter than the control and treatment times don't match u…
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
Thanks James for your helpful response. This particular experimental set up is very common in iPSC studies, where multiple differentiations…
Comment: DESeq2 test for synergistic vs additive effects by Jay • 0
Why is TrtAB - TrtA - TrtB + Control "not really a thing"? i came to this forum answer when attempting to use EdgeR to answer a similar que…
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Votes
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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