Showing : ComBat • reset
1
vote
2
replies
113
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
9 days ago • updated 2 days ago takemoto • 0
0
votes
1
reply
97
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 6 weeks ago by 45k • written 6 weeks ago by • 0
0
votes
4
replies
1.1k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
8 months ago NewBioInfo • 0
4
votes
4
replies
386
views
Combat and dds Object
DESeq2 combat
updated 9 months ago by 3.5k • written 9 months ago by ▴ 20
0
votes
0
replies
246
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
14 months ago joannew • 0
1
vote
3
replies
432
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 14 months ago by 3.5k • written 14 months ago by • 0
1
vote
8
replies
552
views
Error in running Combat function
sva ComBat
updated 16 months ago by 3.5k • written 16 months ago by ▴ 10
0
votes
5
replies
405
views
Variable of interest in combat correction
sva combat
updated 19 months ago by 60k • written 19 months ago by ▴ 10
0
votes
3
replies
368
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 20 months ago by 3.5k • written 20 months ago by • 0
7
votes
6
replies
504
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 2.1 years ago by ▴ 840 • written 2.1 years ago by ▴ 10
1
vote
2
replies
340
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 2.3 years ago by 45k • written 2.4 years ago by • 0
0
votes
0
replies
819
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
2.4 years ago anne.bozack • 0
0
votes
1
reply
356
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 2.5 years ago by 3.5k • written 2.5 years ago by • 0
0
votes
1
reply
368
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 2.5 years ago by ▴ 840 • written 2.5 years ago by ▴ 10
0
votes
3
replies
426
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
8
votes
18
replies
6.7k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 15 months ago by • 0 • written 2.6 years ago by ▴ 10
2
votes
2
replies
579
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 2.6 years ago by 37k • written 2.6 years ago by ▴ 10
2
votes
3
replies
461
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 2.7 years ago by ★ 1.0k • written 2.7 years ago by ▴ 50
0
votes
2
replies
392
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 2.8 years ago by 37k • written 2.8 years ago by • 0
0
votes
0
replies
349
views
The correct specification of the model matrix to ComBat
ComBat sva
2.8 years ago Sam ▴ 10
0
votes
6
replies
995
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by ▴ 640
7
votes
4
replies
2.4k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.9 years ago by 45k • written 2.9 years ago by ▴ 640
4
votes
16
replies
1.2k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 3.0 years ago by 37k • written 3.0 years ago by ▴ 10
3
votes
12
replies
1.6k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 3.1 years ago by 60k • written 3.1 years ago by ▴ 10
0
votes
0
replies
420
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 3.7 years ago by 45k • written 3.7 years ago by • 0
0
votes
2
replies
781
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 3.7 years ago by 37k • written 3.7 years ago by • 0
0
votes
0
replies
459
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
3.7 years ago jmsendoya • 0
0
votes
1
reply
994
views
A problem in using Combat
sva combat
updated 3.9 years ago by ▴ 840 • written 3.9 years ago by • 0
1
vote
1
reply
1.6k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 4.3 years ago by 45k • written 7.2 years ago by ▴ 130
1
vote
9
replies
1.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
4.3 years ago jaro.slamecka ▴ 130
0
votes
8
replies
1.5k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 4.5 years ago by • 0 • written 6.8 years ago by • 0
0
votes
0
replies
598
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
4.6 years ago Eddie Imada • 0
0
votes
1
reply
620
views
Combat prior plots good enough?
combat combat sva
4.6 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
1.4k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by • 0
1
vote
5
replies
3.4k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 4.7 years ago by ★ 27k • written 4.7 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 4.8 years ago by 60k • written 4.8 years ago by • 0
0
votes
0
replies
944
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
4.8 years ago DataFanatic • 0
0
votes
4
replies
1.5k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 5.0 years ago by 37k • written 5.0 years ago by • 0
0
votes
0
replies
840
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
5.1 years ago svlachavas ▴ 780
1
vote
1
reply
635
views
How to interpret the SVA results
SVA combat RNA-seq
updated 5.2 years ago by 60k • written 5.2 years ago by • 0
10
votes
4
replies
1.8k
views
Adjust for multiple batches using combat
combat sva limma
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
3
votes
4
replies
1.9k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 5.3 years ago by 37k • written 5.3 years ago by ▴ 10
0
votes
0
replies
696
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
5.3 years ago Ryan C. Thompson 7.8k
0
votes
6
replies
997
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
5.6 years ago User34591 • 0
5
votes
2
replies
6.1k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by ▴ 30
5
votes
3
replies
2.7k
views
about SVA: matrix of corrected expression values
SVA COMBAT
5.7 years ago Bogdan ▴ 640
3
votes
8
replies
1.4k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 5.7 years ago by ▴ 30 • written 5.7 years ago by • 0
13
votes
2
replies
2.3k
views
voom with combat
limma voom combat batch effect
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 10
0
votes
1
reply
724
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 5.9 years ago by ▴ 400 • written 5.9 years ago by ▴ 780
48
votes
20
replies
30k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 6.0 years ago by • 0 • written 6.5 years ago by ▴ 100
50 results • Page 1 of 1
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Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
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Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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