Showing : BatchEffect • reset
6
votes
7
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1.9k
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Batch effect with one sample being in two batches
BatchEffect DESeq2
23 months ago lmrogers34 ▴ 10
6
votes
4
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11k
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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
6
votes
6
replies
1.4k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
6
votes
4
replies
4.1k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
5
votes
2
replies
780
views
Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
4
votes
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
replies
1.9k
views
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
3
votes
6
replies
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
3
votes
6
replies
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 7.6 years ago by ▴ 50 • written 7.6 years ago by ▴ 10
3
votes
2
replies
755
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
3
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5
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878
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
4
replies
885
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
2
votes
4
replies
1.5k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
13 months ago vk • 0
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
3
replies
2.8k
views
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
2
votes
4
replies
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
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 3.5 years ago by ▴ 10
2
votes
2
replies
993
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
2
votes
4
replies
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
1
reply
1.5k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
4
replies
662
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 5 months ago by 50k • written 5 months ago by • 0
2
votes
3
replies
1.2k
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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
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
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 26 days ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
913
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
2
votes
2
replies
977
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
2
votes
2
replies
897
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 30
2
votes
1
reply
272
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
2
votes
3
replies
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
2
votes
9
replies
408
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
2
replies
805
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 10
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
1
vote
2
replies
987
views
Batch effect between biological replicates
BatchEffect DESeq2
12 months ago gtechbio ▴ 10
1
vote
1
reply
503
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
15
replies
2.5k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.1 years ago demisa • 0
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
1
vote
5
replies
2.7k
views
Deseq2 - removing batch effect
BatchEffect DESeq2
updated 3.1 years ago by ★ 3.9k • written 3.1 years 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 ▴ 50
1
vote
1
reply
710
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 23 months ago by 42k • written 23 months ago by • 0
1
vote
0
replies
682
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
1
vote
1
reply
465
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
2
replies
889
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
1
vote
2
replies
902
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
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
1
vote
4
replies
647
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
1
vote
6
replies
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
1
vote
3
replies
963
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
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
1
vote
1
reply
1.7k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
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thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
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I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
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