Showing : combat • reset
0
votes
0
replies
98
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
6 weeks ago joannew • 0
0
votes
3
replies
143
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 8 weeks ago by 2.9k • written 8 weeks ago by • 0
1
vote
8
replies
278
views
Error in running Combat function
sva ComBat
updated 3 months ago by 2.9k • written 3 months ago by ▴ 10
0
votes
5
replies
131
views
Variable of interest in combat correction
sva combat
updated 6 months ago by 56k • written 6 months ago by ▴ 10
0
votes
3
replies
171
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 7 months ago by 2.9k • written 7 months ago by • 0
7
votes
6
replies
204
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 12 months ago by ▴ 840 • written 12 months ago by ▴ 10
1
vote
2
replies
142
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 15 months ago by 42k • written 15 months ago by • 0
0
votes
0
replies
351
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
16 months ago anne.bozack • 0
0
votes
1
reply
122
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 17 months ago by 2.9k • written 17 months ago by • 0
0
votes
1
reply
169
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 17 months ago by ▴ 840 • written 17 months ago by ▴ 10
0
votes
3
replies
204
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 18 months ago by 25k • written 18 months ago by • 0
4
votes
18
replies
3.2k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 12 weeks ago by • 0 • written 19 months ago by • 0
2
votes
2
replies
257
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 19 months ago by 32k • written 19 months ago by ▴ 10
2
votes
3
replies
257
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 20 months ago by ▴ 710 • written 20 months ago by ▴ 50
0
votes
2
replies
186
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 20 months ago by 32k • written 20 months ago by • 0
0
votes
0
replies
218
views
The correct specification of the model matrix to ComBat
ComBat sva
21 months ago Sam ▴ 10
0
votes
6
replies
672
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 21 months ago by ▴ 260 • written 21 months ago by ▴ 610
7
votes
4
replies
1.3k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 21 months ago by 42k • written 21 months ago by ▴ 610
4
votes
16
replies
357
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 23 months ago by 32k • written 23 months ago by ▴ 10
3
votes
12
replies
918
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.0 years ago by 56k • written 2.0 years ago by ▴ 10
0
votes
0
replies
308
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
2
replies
569
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.6 years ago by 32k • written 2.6 years ago by • 0
0
votes
0
replies
312
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
2.7 years ago jmsendoya • 0
0
votes
1
reply
565
views
A problem in using Combat
sva combat
updated 2.9 years ago by ▴ 840 • written 2.9 years ago by • 0
1
vote
1
reply
1.4k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 3.3 years ago by 42k • written 6.1 years ago by ▴ 130
1
vote
9
replies
1.0k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
3.3 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.1k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 3.4 years ago by • 0 • written 5.8 years ago by • 0
0
votes
0
replies
476
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
3.5 years ago elim • 0
0
votes
1
reply
449
views
Combat prior plots good enough?
combat combat sva
3.6 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.0k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 3.6 years ago by ▴ 840 • written 3.6 years ago by • 0
1
vote
5
replies
2.3k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 3.6 years ago by ★ 26k • written 3.6 years ago by ▴ 20
1
vote
1
reply
1.1k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 3.8 years ago by 56k • written 3.8 years ago by • 0
0
votes
0
replies
820
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
3.8 years ago DataFanatic • 0
0
votes
4
replies
1.2k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 3.9 years ago by 32k • written 3.9 years ago by • 0
0
votes
0
replies
672
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
4.0 years ago svlachavas ▴ 780
1
vote
1
reply
517
views
How to interpret the SVA results
SVA combat RNA-seq
updated 4.1 years ago by 56k • written 4.1 years ago by • 0
10
votes
4
replies
1.4k
views
Adjust for multiple batches using combat
combat sva limma
updated 4.2 years ago by ★ 26k • written 4.2 years ago by • 0
3
votes
4
replies
1.4k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 4.2 years ago by 32k • written 4.2 years ago by ▴ 10
0
votes
0
replies
526
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
4.2 years ago Ryan C. Thompson 7.6k
0
votes
6
replies
657
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
4.5 years ago User34591 • 0
4
votes
2
replies
5.5k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by ▴ 20
5
votes
3
replies
2.2k
views
about SVA: matrix of corrected expression values
SVA COMBAT
4.6 years ago Bogdan ▴ 610
3
votes
8
replies
1.1k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 4.7 years ago by ▴ 30 • written 4.7 years ago by • 0
13
votes
2
replies
2.1k
views
voom with combat
limma voom combat batch effect
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 10
0
votes
1
reply
567
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 4.8 years ago by ▴ 390 • written 4.8 years ago by ▴ 780
44
votes
20
replies
25k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 4.9 years ago by • 0 • written 5.4 years ago by ▴ 100
2
votes
3
replies
762
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 5.0 years ago by ▴ 390 • written 5.0 years ago by • 0
0
votes
0
replies
570
views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
5.0 years ago John Townsend ▴ 20
7
votes
3
replies
2.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 5.0 years ago by ▴ 840 • written 5.1 years ago by ▴ 20
10
votes
10
replies
2.4k
views
Method for batch correction
combat sva limma
updated 5.1 years ago by ▴ 110 • written 5.1 years ago by ▴ 50
77 results • Page 1 of 2
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Answer: DiffBind by Rory Stark ★ 3.8k
I'll answer the second question first. You should not accessing the `$binding` matrix directly -- the chromosome names are factor numbers,…
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You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…
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If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…
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Thank you very much for the explanation. Making it more precise. Could I analyze and normalize all samples from a dataset even though I had…
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What does dba.PCA in DiffBind exactly do?
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Effect of feature number on adjusted p-values
Effect of feature number on adjusted p-values
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