Showing : combat • reset
0
votes
4
replies
532
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3 months ago NewBioInfo • 0
4
votes
4
replies
273
views
Combat and dds Object
DESeq2 combat
updated 5 months ago by 3.4k • written 5 months ago by ▴ 20
0
votes
0
replies
203
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
9 months ago joannew • 0
0
votes
3
replies
344
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 10 months ago by 3.4k • written 10 months ago by • 0
1
vote
8
replies
474
views
Error in running Combat function
sva ComBat
updated 11 months ago by 3.4k • written 12 months ago by ▴ 10
0
votes
5
replies
333
views
Variable of interest in combat correction
sva combat
updated 14 months ago by 58k • written 14 months ago by ▴ 10
0
votes
3
replies
312
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 15 months ago by 3.4k • written 15 months ago by • 0
7
votes
6
replies
410
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 20 months ago by ▴ 840 • written 20 months ago by ▴ 10
1
vote
2
replies
284
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 24 months ago by 44k • written 24 months ago by • 0
0
votes
0
replies
641
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
2.0 years ago anne.bozack • 0
0
votes
1
reply
271
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 2.1 years ago by 3.4k • written 2.1 years ago by • 0
0
votes
1
reply
315
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 2.1 years ago by ▴ 840 • written 2.1 years ago by ▴ 10
0
votes
3
replies
363
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 2.2 years ago by 25k • written 2.2 years ago by • 0
8
votes
18
replies
5.6k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 11 months ago by • 0 • written 2.3 years ago by ▴ 10
2
votes
2
replies
455
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 2.3 years ago by 35k • written 2.3 years ago by ▴ 10
2
votes
3
replies
401
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 2.4 years ago by ▴ 970 • written 2.4 years ago by ▴ 50
0
votes
2
replies
315
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 2.4 years ago by 35k • written 2.4 years ago by • 0
0
votes
0
replies
318
views
The correct specification of the model matrix to ComBat
ComBat sva
2.4 years ago Sam ▴ 10
0
votes
6
replies
898
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 2.4 years ago by ▴ 260 • written 2.5 years ago by ▴ 620
7
votes
4
replies
1.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.5 years ago by 44k • written 2.5 years ago by ▴ 620
4
votes
16
replies
774
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 2.6 years ago by 35k • written 2.6 years ago by ▴ 10
3
votes
12
replies
1.4k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.7 years ago by 58k • written 2.7 years ago by ▴ 10
0
votes
0
replies
386
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 3.3 years ago by 44k • written 3.3 years ago by • 0
0
votes
2
replies
704
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
0
votes
0
replies
412
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
3.4 years ago jmsendoya • 0
0
votes
1
reply
803
views
A problem in using Combat
sva combat
updated 3.6 years ago by ▴ 840 • written 3.6 years ago by • 0
1
vote
1
reply
1.6k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 4.0 years ago by 44k • written 6.8 years ago by ▴ 130
1
vote
9
replies
1.3k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
4.0 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.3k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 4.1 years ago by • 0 • written 6.5 years ago by • 0
0
votes
0
replies
557
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
4.2 years ago Eddie Imada • 0
0
votes
1
reply
572
views
Combat prior plots good enough?
combat combat sva
4.3 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.3k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 4.3 years ago by ▴ 840 • written 4.3 years ago by • 0
1
vote
5
replies
3.0k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ▴ 20
1
vote
1
reply
1.3k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 4.5 years ago by 58k • written 4.5 years ago by • 0
0
votes
0
replies
907
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
4.5 years ago DataFanatic • 0
0
votes
4
replies
1.4k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 4.6 years ago by 35k • written 4.6 years ago by • 0
0
votes
0
replies
793
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
4.7 years ago svlachavas ▴ 780
1
vote
1
reply
596
views
How to interpret the SVA results
SVA combat RNA-seq
updated 4.8 years ago by 58k • written 4.8 years ago by • 0
10
votes
4
replies
1.7k
views
Adjust for multiple batches using combat
combat sva limma
updated 4.9 years ago by ★ 27k • written 4.9 years ago by • 0
3
votes
4
replies
1.7k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 4.9 years ago by 35k • written 4.9 years ago by ▴ 10
0
votes
0
replies
663
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
4.9 years ago Ryan C. Thompson 7.7k
0
votes
6
replies
910
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
5.2 years ago User34591 • 0
5
votes
2
replies
5.8k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 5.2 years ago by ▴ 70 • written 5.2 years ago by ▴ 30
5
votes
3
replies
2.5k
views
about SVA: matrix of corrected expression values
SVA COMBAT
5.3 years ago Bogdan ▴ 620
3
votes
8
replies
1.4k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 5.4 years ago by ▴ 30 • written 5.4 years ago by • 0
13
votes
2
replies
2.2k
views
voom with combat
limma voom combat batch effect
updated 5.5 years ago by 44k • written 5.5 years ago by ▴ 10
0
votes
1
reply
689
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 5.5 years ago by ▴ 390 • written 5.5 years ago by ▴ 780
45
votes
20
replies
28k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.6 years ago by • 0 • written 6.1 years ago by ▴ 100
2
votes
3
replies
908
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 5.7 years ago by ▴ 390 • written 5.7 years ago by • 0
0
votes
0
replies
653
views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
5.7 years ago John Townsend ▴ 20
50 results • Page 1 of 1
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Comment: Cannot install Phyloseq and dada2 by Guido Hooiveld ★ 3.2k
Did you notice this message:? Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.0.0/libra…
Comment: Use of shrunken LFCs to address questions about the distribution of LFCs between by i.sudbery ▴ 20
Thanks Mike. I might have a play with stratifying by expression level. One reason I wasn't looking at gene set testing is that its the nul…
Answer: submitting a BSgenome package by deisianyufg • 0
From my Github repository. I am sorry, I thought the package was already released and realize now that is still only in my github reposito…
Comment: PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp by swbarnes2 ▴ 970
Is the one plot a mirror image of the other?
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between by Michael Love 35k
hi Ian, Great question, and good to be concerned that the mean expression may be a confounder for either analysis, Why not stratify your…
Votes
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between
Answer: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
Comment: submitting a BSgenome package
Answer: rlog vs vst for outlier identification
Answer: DESeq2 median of ratios normalization for signature score calculation
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