Showing : ComBat • reset
1
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2
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55
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Error in running Combat function
sva ComBat
5 days ago • updated 4 days ago Reza • 10
0
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5
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80
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Variable of interest in combat correction
sva combat
10 weeks ago ch_el • 10 • updated 10 weeks ago James W. MacDonald 55k
0
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3
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106
Views
Extracting a subset of samples following SVA
Combat SVA Limma
3 months ago jonellevillar • 0 • updated 3 months ago Kevin Blighe 2.3k
7
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6
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129
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sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
8 months ago Zach Roe • 10 • updated 8 months ago W. Evan Johnson • 830
1
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2
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97
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Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
12 months ago vizio12341337 • 0 • updated 12 months ago Gordon Smyth 41k
0
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0
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245
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
12 months ago anne.bozack • 0
0
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1
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97
Views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
13 months ago lucasmiranda42 • 0 • updated 13 months ago Kevin Blighe 2.3k
0
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1
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124
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problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
13 months ago modarzi • 10 • updated 13 months ago W. Evan Johnson • 830
0
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3
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154
Views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
14 months ago dhwani2410 • 0 • updated 14 months ago Martin Morgan 25k
4
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17
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2.1k
Views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
15 months ago rajeshparmar4 • 0 • updated 15 months ago Yuqing Zhang • 20
2
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2
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198
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Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
15 months ago Sam • 0 • updated 15 months ago Michael Love 31k
2
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3
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204
Views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
16 months ago ag1805x • 50 • updated 16 months ago swbarnes2 • 620
0
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2
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147
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Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
17 months ago ege.dedeoglu • 0 • updated 17 months ago Michael Love 31k
0
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0
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175
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The correct specification of the model matrix to ComBat
ComBat sva
17 months ago Sam • 0
0
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6
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582
Views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
17 months ago Bogdan • 610 • updated 17 months ago Andrew_McDavid • 260
7
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4
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1.1k
Views
correcting the batch effects in Limma and SVA
limma combat sva
18 months ago Bogdan • 610 • updated 18 months ago Gordon Smyth 41k
4
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16
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266
Views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
19 months ago joseale2310 • 10 • updated 19 months ago Michael Love 31k
3
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12
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715
Views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
21 months ago hackingfactory • 10 • updated 21 months ago James W. MacDonald 55k
0
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0
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280
Views
ComBat: missing peptide for one batch
batch effect missing value Combat
2.3 years ago hjleeab • 0 • updated 2.3 years ago Gordon Smyth 41k
0
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2
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495
Views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
2.3 years ago grimmerucsf • 0 • updated 2.3 years ago Michael Love 31k
0
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0
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277
Views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
2.4 years ago jmsendoya • 0
0
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1
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477
Views
A problem in using Combat
sva combat
2.6 years ago linw • 0 • updated 2.6 years ago W. Evan Johnson • 830
1
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1
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1.3k
Views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
5.8 years ago jaro.slamecka • 130 • updated 3.0 years ago Gordon Smyth 41k
1
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9
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908
Views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
3.0 years ago jaro.slamecka • 130
0
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8
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1.1k
Views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
5.5 years ago radhikaraheja • 0 • updated 3.1 years ago shaymaa_s_elgaafary • 0
0
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0
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437
Views
SVA/Combat without fitting an intercept
sva combat batch effect limma
3.2 years ago elim • 0
0
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1
Reply
412
Views
Combat prior plots good enough?
combat combat sva
3.3 years ago Miss Agnieszka Aleksandra Golicz • 40
2
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5
Replies
909
Views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
3.3 years ago JMallory • 0 • updated 3.3 years ago W. Evan Johnson • 830
1
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5
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2.1k
Views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
3.3 years ago rmf • 20 • updated 3.3 years ago Aaron Lun ♦ 26k
1
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1
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1.1k
Views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
3.5 years ago DataFanatic • 0 • updated 3.5 years ago James W. MacDonald 55k
0
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0
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795
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Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
3.5 years ago DataFanatic • 0
0
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4
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1.2k
Views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
3.6 years ago noname • 0 • updated 3.6 years ago Michael Love 31k
0
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0
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628
Views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
3.7 years ago svlachavas • 770
1
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1
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489
Views
How to interpret the SVA results
SVA combat RNA-seq
3.8 years ago xie186 • 0 • updated 3.8 years ago James W. MacDonald 55k
8
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4
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1.3k
Views
Adjust for multiple batches using combat
combat sva limma
3.9 years ago juls • 0 • updated 3.9 years ago Aaron Lun ♦ 26k
3
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4
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1.3k
Views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
3.9 years ago g.atla • 10 • updated 3.9 years ago Michael Love 31k
0
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0
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498
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How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
3.9 years ago Ryan C. Thompson 7.6k
0
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6
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595
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Combine RNAseq datasets vst + Combat
combat vst deseq2
4.2 years ago User34591 • 0
4
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2
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5.3k
Views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
4.2 years ago kerrypop • 20 • updated 4.2 years ago polemiraza • 60
5
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3
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2.0k
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about SVA: matrix of corrected expression values
SVA COMBAT
4.3 years ago Bogdan • 610
3
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8
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987
Views
What type of data normalization for multiple microarrays?
normalization microarray combat
4.4 years ago Ewelina Dratkiewicz • 0 • updated 4.4 years ago manimaran_1975 • 30
13
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2
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2.0k
Views
voom with combat
limma voom combat batch effect
4.5 years ago eldronzhou • 10 • updated 4.5 years ago Gordon Smyth 41k
0
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1
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539
Views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
4.5 years ago svlachavas • 770 • updated 4.5 years ago chris86 • 390
44
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20
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24k
Views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
5.1 years ago AB • 100 • updated 4.6 years ago adam • 0
2
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3
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720
Views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
4.7 years ago TP • 0 • updated 4.7 years ago chris86 • 390
0
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0
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547
Views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
4.7 years ago John Townsend • 20
7
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3
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2.0k
Views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
4.7 years ago John Townsend • 20 • updated 4.7 years ago W. Evan Johnson • 830
10
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10
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2.3k
Views
Method for batch correction
combat sva limma
4.8 years ago AST • 50 • updated 4.8 years ago Vegard Nygaard • 110
0
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1
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502
Views
Error ,when I use "pa.calls" function on my dataset
panp Combat
4.8 years ago Shamim Sarhadi • 20
1
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2
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1.1k
Views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
5.0 years ago svlachavas • 770 • updated 5.0 years ago W. Evan Johnson • 830
75 results • Page 1 of 2
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Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to anal by larissa.stanberry • 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
Votes
A: Interpreting the results from lfcShrink() with apeglm in DESeq2
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
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