Showing : ComBat • reset
0
votes
4
replies
395
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
25 days ago • updated 23 days ago Lucy ▴ 60
5
votes
2
replies
729
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
0
votes
0
replies
474
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
13 months ago Jitendra ▴ 10
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
0
votes
1
reply
916
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
1
vote
4
replies
5.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.6 years ago NewBioInfo ▴ 10
5
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8
replies
2.4k
views
Combat and dds Object
DESeq2 combat
updated 14 months ago by ★ 4.0k • written 2.7 years ago by ▴ 40
0
votes
0
replies
690
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
3.1 years ago joannew • 0
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva combat
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
7
votes
6
replies
1.6k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.0 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
1
vote
2
replies
924
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 4.3 years ago by 50k • written 4.3 years ago by • 0
0
votes
0
replies
1.9k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
4.3 years ago anne.bozack • 0
0
votes
1
reply
966
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 4.4 years ago by ★ 3.9k • written 4.4 years ago by • 0
0
votes
1
reply
884
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 4.4 years ago by ▴ 850 • written 4.4 years ago by ▴ 10
0
votes
3
replies
985
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 4.6 years ago by 41k • written 4.6 years ago by ▴ 10
2
votes
3
replies
1.0k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by ▴ 80
0
votes
2
replies
1.1k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
0
replies
807
views
The correct specification of the model matrix to ComBat
ComBat sva
4.7 years ago Sam ▴ 10
0
votes
6
replies
1.8k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 670
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 4.8 years ago by 50k • written 4.8 years ago by ▴ 670
4
votes
16
replies
4.5k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 10
3
votes
12
replies
3.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
0
replies
801
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
0
votes
0
replies
922
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
5.6 years ago jmsendoya • 0
0
votes
1
reply
1.8k
views
A problem in using Combat
sva combat
updated 5.8 years ago by ▴ 850 • written 5.8 years ago by • 0
1
vote
1
reply
2.1k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.2 years ago by 50k • written 9.1 years ago by ▴ 140
1
vote
9
replies
2.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
6.2 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.3k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 6.4 years ago by • 0 • written 8.7 years ago by • 0
0
votes
0
replies
1.1k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
6.5 years ago Eddie Imada • 0
0
votes
1
reply
1.2k
views
Combat prior plots good enough?
combat combat sva
6.6 years ago • updated 6.5 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
2.8k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 6.6 years ago by ▴ 850 • written 6.6 years ago by • 0
2
votes
5
replies
5.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
1
vote
1
reply
1.8k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 6.7 years ago by 65k • written 6.7 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
6.7 years ago DataFanatic ▴ 10
0
votes
4
replies
2.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
0
votes
0
replies
1.3k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.0 years ago svlachavas ▴ 830
1
vote
1
reply
1.1k
views
How to interpret the SVA results
SVA combat RNA-seq
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
10
votes
4
replies
2.9k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
7.5 years ago User34591 • 0
5
votes
2
replies
7.2k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 7.5 years ago by ▴ 70 • written 7.5 years ago by ▴ 30
5
votes
3
replies
3.8k
views
about SVA: matrix of corrected expression values
SVA COMBAT
7.6 years ago Bogdan ▴ 670
3
votes
8
replies
2.3k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 7.6 years ago by ▴ 30 • written 7.6 years ago by • 0
50 results • Page 1 of 1
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Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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