Showing : combat • reset
0
votes
4
replies
949
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
10 months ago Lucy ▴ 60
5
votes
2
replies
1.9k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
16 months ago Federico ▴ 10
0
votes
0
replies
678
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
22 months ago Jitendra ▴ 10
1
vote
2
replies
2.1k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.7 years ago takemoto • 0
0
votes
1
reply
1.4k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
1
vote
4
replies
7.4k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.4 years ago NewBioInfo ▴ 10
5
votes
8
replies
3.4k
views
Combat and dds Object
DESeq2 combat
updated 24 months ago by ★ 4.6k • written 3.5 years ago by ▴ 50
0
votes
0
replies
898
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
3.8 years ago joannew • 0
1
vote
4
replies
2.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 15 months ago by • 0 • written 3.9 years ago by • 0
1
vote
8
replies
1.8k
views
Error in running Combat function
sva ComBat
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 10
0
votes
5
replies
1.4k
views
Variable of interest in combat correction
sva combat
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.3 years ago by ★ 4.0k • written 4.4 years ago by • 0
7
votes
6
replies
2.3k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
0
votes
0
replies
2.5k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.1 years ago anne.bozack • 0
0
votes
1
reply
1.3k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.1 years ago by ★ 4.0k • written 5.2 years ago by • 0
0
votes
1
reply
1.1k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.2 years ago by ▴ 870 • written 5.2 years ago by ▴ 10
0
votes
3
replies
1.2k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
8
votes
18
replies
14k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.0 years ago by • 0 • written 5.3 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 5.4 years ago by ★ 1.4k • written 5.4 years ago by ▴ 80
0
votes
2
replies
1.4k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
0
replies
970
views
The correct specification of the model matrix to ComBat
ComBat sva
5.5 years ago Sam ▴ 10
0
votes
6
replies
2.1k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 5.5 years ago by ▴ 270 • written 5.5 years ago by ▴ 670
8
votes
4
replies
4.6k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 670
4
votes
16
replies
6.1k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
3
votes
12
replies
4.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
0
votes
0
replies
984
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.3 years ago by 52k • written 6.3 years ago by • 0
0
votes
2
replies
1.7k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
0
replies
1.1k
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
6.4 years ago jmsendoya • 0
0
votes
1
reply
2.2k
views
A problem in using Combat
sva combat
updated 6.6 years ago by ▴ 870 • written 6.6 years ago by • 0
1
vote
1
reply
2.3k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 7.0 years ago by 52k • written 9.9 years ago by ▴ 140
1
vote
9
replies
3.1k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
7.0 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.6k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 7.1 years ago by • 0 • written 9.5 years ago by • 0
0
votes
0
replies
1.3k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
7.3 years ago Eddie Imada • 0
0
votes
1
reply
1.4k
views
Combat prior plots good enough?
combat combat sva
7.3 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
3.4k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.3 years ago by ▴ 870 • written 7.3 years ago by • 0
2
votes
5
replies
6.9k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 7.5 years ago by 67k • written 7.5 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
7.5 years ago DataFanatic ▴ 10
0
votes
4
replies
2.7k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
0
replies
1.4k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.8 years ago • updated 7.7 years ago svlachavas ▴ 840
10
votes
4
replies
3.4k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
3
votes
4
replies
3.2k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
0
votes
0
replies
1.3k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
8.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
6
replies
2.0k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
8.3 years ago User34591 • 0
5
votes
2
replies
7.7k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 8.3 years ago by ▴ 70 • written 8.3 years ago by ▴ 30
5
votes
3
replies
4.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.3 years ago Bogdan ▴ 670
3
votes
8
replies
2.8k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by • 0
14
votes
2
replies
3.6k
views
voom with combat
limma voom combat batch effect
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 10
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
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