Showing : batcheffect • reset
6
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.2 years ago by ▴ 10
2
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4
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5.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
6
votes
4
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4.0k
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Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 830
3
votes
6
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3.0k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 8.9 years ago by • 0 • written 9.5 years ago by ▴ 10
2
votes
3
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2.8k
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Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 9.0 years ago by 65k • written 9.0 years ago by ▴ 830
1
vote
5
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2.7k
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Deseq2 - removing batch effect
BatchEffect DESeq2
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
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15
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2.5k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.1 years ago demisa • 0
0
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3
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2.3k
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Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
3
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6
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2.3k
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is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 7.5 years ago by ▴ 50 • written 7.5 years ago by ▴ 10
4
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10
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2.0k
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Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 7.0 years ago by 50k • written 7.0 years ago by ▴ 20
3
votes
10
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1.9k
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
19 months ago • updated 18 months ago eve.olszanowski • 0
1
vote
5
replies
1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 9.1 years ago by ▴ 830 • written 9.1 years ago by ▴ 830
6
votes
7
replies
1.8k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
23 months ago • updated 22 months ago lmrogers34 ▴ 10
1
vote
1
reply
1.7k
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batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
1
vote
6
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1.7k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 110
2
votes
1
reply
1.6k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
2
votes
4
replies
1.5k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
2
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1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
6
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6
replies
1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
2
votes
5
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1.3k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 9 months ago by • 0
1
vote
1
reply
1.3k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 3.5 years ago by 42k • written 3.5 years ago by ▴ 40
2
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1
reply
1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 23 months ago by 50k • written 23 months ago by ▴ 30
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
11.1 years ago Daniel Emden ▴ 10
2
votes
4
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1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 42k • written 2.9 years ago by • 0
2
votes
3
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1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
1
vote
5
replies
1.1k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 10
2
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3
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1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 9 months ago by 65k • written 9 months ago by ▴ 10
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by ▴ 30
0
votes
2
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1.0k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.3 years ago by ★ 13k • written 2.4 years ago by • 0
2
votes
2
replies
1.0k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 3.4 years ago by ▴ 350 • written 3.4 years ago by ▴ 10
1
vote
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
2
votes
2
replies
987
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
1
vote
2
replies
982
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
votes
1
reply
975
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 42k • written 20 months ago by • 0
2
votes
2
replies
971
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
2.6 years ago p.joshi ▴ 40
1
vote
3
replies
955
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.5 years ago by 50k • written 3.5 years ago by • 0
0
votes
1
reply
946
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by • 0
0
votes
2
replies
943
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
0
votes
1
reply
939
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
0
votes
2
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933
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by ▴ 120
0
votes
4
replies
908
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
2
votes
3
replies
896
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
1
vote
2
replies
896
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.3k • written 18 months ago by • 0
1
vote
2
replies
887
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
2.6 years ago • updated 2.3 years ago zeegzaag • 0
2
votes
2
replies
886
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
0
votes
1
reply
878
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 21 months ago by 50k • written 21 months ago by • 0
3
votes
4
replies
878
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
5
replies
861
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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