Showing : ComBat • reset
1
vote
1
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804
views
ComBat with repeated measures
ComBat sva
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
0
votes
4
replies
1.2k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
13 months ago Lucy ▴ 60
5
votes
2
replies
2.4k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
19 months ago Federico ▴ 10
0
votes
0
replies
746
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
2.2 years ago Jitendra ▴ 10
1
vote
2
replies
2.3k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3.0 years ago takemoto • 0
0
votes
1
reply
1.7k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.1 years ago by 52k • written 3.1 years ago by • 0
1
vote
4
replies
8.2k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.7 years ago NewBioInfo ▴ 10
5
votes
8
replies
3.9k
views
Combat and dds Object
DESeq2 combat
updated 2.3 years ago by ★ 4.8k • written 3.8 years ago by ▴ 50
0
votes
0
replies
955
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
4.1 years ago joannew • 0
1
vote
4
replies
3.3k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 19 months ago by • 0 • written 4.2 years ago by • 0
1
vote
8
replies
2.0k
views
Error in running Combat function
sva ComBat
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Variable of interest in combat correction
sva combat
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.5k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
7
votes
6
replies
2.5k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 5.0 years ago by ▴ 870 • written 5.0 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
0
votes
0
replies
2.7k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.4 years ago anne.bozack • 0
0
votes
1
reply
1.5k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
1
reply
1.2k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.4 years ago by ▴ 870 • written 5.4 years ago by ▴ 10
0
votes
3
replies
1.3k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
8
votes
18
replies
15k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.3 years ago by • 0 • written 5.6 years ago by ▴ 10
2
votes
2
replies
1.9k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by ▴ 80
0
votes
2
replies
1.6k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
0
replies
1.0k
views
The correct specification of the model matrix to ComBat
ComBat sva
5.8 years ago Sam ▴ 10
0
votes
6
replies
2.2k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by ▴ 670
8
votes
4
replies
5.1k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 670
4
votes
16
replies
6.9k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
3
votes
12
replies
4.6k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
0
votes
0
replies
1.0k
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
0
votes
2
replies
1.8k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
1.2k
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
6.7 years ago jmsendoya • 0
0
votes
1
reply
2.5k
views
A problem in using Combat
sva combat
updated 6.9 years ago by ▴ 870 • written 6.9 years ago by • 0
1
vote
1
reply
2.3k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 7.3 years ago by 52k • written 10.2 years ago by ▴ 140
1
vote
9
replies
3.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
7.3 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.8k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 7.4 years ago by • 0 • written 9.8 years ago by • 0
0
votes
0
replies
1.3k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
7.6 years ago Eddie Imada • 0
0
votes
1
reply
1.5k
views
Combat prior plots good enough?
combat combat sva
7.6 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
3.7k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.6 years ago by ▴ 870 • written 7.6 years ago by • 0
2
votes
5
replies
7.5k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
1
vote
1
reply
2.2k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
7.8 years ago DataFanatic ▴ 10
0
votes
4
replies
2.9k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
votes
0
replies
1.5k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
8.0 years ago svlachavas ▴ 840
10
votes
4
replies
3.7k
views
Adjust for multiple batches using combat
combat sva limma
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
3
votes
4
replies
3.5k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
0
replies
1.4k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
8.3 years ago Ryan C. Thompson ★ 7.9k
0
votes
6
replies
2.2k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
8.6 years ago User34591 • 0
5
votes
2
replies
8.2k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 8.6 years ago by ▴ 70 • written 8.6 years ago by ▴ 30
5
votes
3
replies
4.4k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.6 years ago Bogdan ▴ 670
3
votes
8
replies
3.0k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 8.7 years ago by ▴ 30 • written 8.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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