Showing : ComBat • reset
0
votes
0
replies
103
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
11 weeks ago Jitendra ▴ 10
1
vote
2
replies
777
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
12 months ago takemoto • 0
0
votes
1
reply
416
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 13 months ago by 47k • written 13 months ago by • 0
1
vote
4
replies
3.5k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
20 months ago NewBioInfo ▴ 10
5
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8
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1.3k
views
Combat and dds Object
DESeq2 combat
updated 4 months ago by ★ 2.9k • written 22 months ago by ▴ 20
0
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0
replies
418
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
2.2 years ago joannew • 0
1
vote
3
replies
938
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
1
vote
8
replies
992
views
Error in running Combat function
sva ComBat
updated 2.4 years ago by 3.8k • written 2.4 years ago by ▴ 10
0
votes
5
replies
665
views
Variable of interest in combat correction
sva combat
updated 2.6 years ago by 63k • written 2.6 years ago by ▴ 10
0
votes
3
replies
623
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 2.7 years ago by 3.8k • written 2.7 years ago by • 0
7
votes
6
replies
984
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 3.1 years ago by ▴ 840 • written 3.1 years ago by ▴ 10
1
vote
2
replies
586
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 3.4 years ago by 47k • written 3.4 years ago by • 0
0
votes
0
replies
1.3k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.4 years ago anne.bozack • 0
0
votes
1
reply
616
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 3.5 years ago by 3.8k • written 3.5 years ago by • 0
0
votes
1
reply
581
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 3.5 years ago by ▴ 840 • written 3.5 years ago by ▴ 10
0
votes
3
replies
667
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
8
votes
18
replies
9.2k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 2.3 years ago by • 0 • written 3.7 years ago by ▴ 10
2
votes
2
replies
897
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 3.7 years ago by 40k • written 3.7 years ago by ▴ 10
2
votes
3
replies
684
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 3.8 years ago by ★ 1.2k • written 3.8 years ago by ▴ 80
0
votes
2
replies
771
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
0
votes
0
replies
532
views
The correct specification of the model matrix to ComBat
ComBat sva
3.8 years ago Sam ▴ 10
0
votes
6
replies
1.3k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 3.8 years ago by ▴ 270 • written 3.8 years ago by ▴ 660
7
votes
4
replies
3.2k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 3.9 years ago by 47k • written 3.9 years ago by ▴ 660
4
votes
16
replies
2.8k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 4.0 years ago by 40k • written 4.0 years ago by ▴ 10
3
votes
12
replies
2.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 4.1 years ago by 63k • written 4.1 years ago by ▴ 10
0
votes
0
replies
582
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 4.7 years ago by 47k • written 4.7 years ago by • 0
0
votes
2
replies
1.0k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 4.7 years ago by 40k • written 4.7 years ago by • 0
0
votes
0
replies
656
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
4.7 years ago jmsendoya • 0
0
votes
1
reply
1.3k
views
A problem in using Combat
sva combat
updated 4.9 years ago by ▴ 840 • written 4.9 years ago by • 0
1
vote
1
reply
1.8k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 5.4 years ago by 47k • written 8.2 years ago by ▴ 140
1
vote
9
replies
1.8k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
5.4 years ago jaro.slamecka ▴ 140
0
votes
8
replies
1.8k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 5.5 years ago by • 0 • written 7.8 years ago by • 0
0
votes
0
replies
771
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
5.6 years ago Eddie Imada • 0
0
votes
1
reply
810
views
Combat prior plots good enough?
combat combat sva
5.7 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.9k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 5.7 years ago by ▴ 840 • written 5.7 years ago by • 0
2
votes
5
replies
4.6k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 20
1
vote
1
reply
1.5k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 5.8 years ago by 63k • written 5.8 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
5.8 years ago DataFanatic ▴ 10
0
votes
4
replies
1.9k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.0 years ago by 40k • written 6.0 years ago by • 0
0
votes
0
replies
1.0k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
6.1 years ago svlachavas ▴ 810
1
vote
1
reply
791
views
How to interpret the SVA results
SVA combat RNA-seq
updated 6.2 years ago by 63k • written 6.2 years ago by • 0
10
votes
4
replies
2.3k
views
Adjust for multiple batches using combat
combat sva limma
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
3
votes
4
replies
2.3k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 6.3 years ago by 40k • written 6.3 years ago by ▴ 10
0
votes
0
replies
885
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
6.3 years ago Ryan C. Thompson 7.8k
0
votes
6
replies
1.3k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
6.6 years ago User34591 • 0
5
votes
2
replies
6.6k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 6.6 years ago by ▴ 70 • written 6.6 years ago by ▴ 30
5
votes
3
replies
3.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
6.7 years ago Bogdan ▴ 660
3
votes
8
replies
1.8k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 6.7 years ago by ▴ 30 • written 6.8 years ago by • 0
13
votes
2
replies
2.6k
views
voom with combat
limma voom combat batch effect
updated 6.9 years ago by 47k • written 6.9 years ago by ▴ 10
0
votes
1
reply
952
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 6.9 years ago by ▴ 400 • written 6.9 years ago by ▴ 810
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Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
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Comment: DESeq2 on multilevel design variable
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
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