Showing : BatchEffect • reset
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.9 years ago r_grau ▴ 10
1
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2
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1.5k
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
3
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10
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3.1k
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
3.1 years ago eve.olszanowski • 0
1
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2
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1.2k
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
3.1 years ago annamariabugaj ▴ 10
0
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1
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1.8k
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.4k
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Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
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1
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1.1k
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RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
6
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7
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3.3k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
3.5 years ago • updated 3.4 years ago lmrogers34 ▴ 10
2
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1
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2.1k
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removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 70
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1
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1.9k
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Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
1
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1
reply
2.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 70
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0
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760
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Is it possible to do batch correction on Ht-Seq raw counts instead of using normalized counts? What's the difference?
Normalisedcounts Rawcounts Ht-SeqRNAData BatchEffect
3.8 years ago Ety • 0
1
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7
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2.2k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 10
0
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2
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1.5k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.9 years ago by ★ 13k • written 3.9 years ago by • 0
0
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2
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1.6k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.1 years ago m.glymenaki • 0
6
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6
replies
2.3k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
4.1 years ago ary.lech ▴ 10
0
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1
reply
1.5k
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Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
2
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2
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1.7k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
4.2 years ago p.joshi ▴ 40
1
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2
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1.4k
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Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
4.2 years ago • updated 3.9 years ago zeegzaag • 0
1
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3
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3.9k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
2
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4
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1.8k
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.2 years ago by 43k • written 4.5 years ago by • 0
1
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5
replies
4.1k
views
Deseq2 - removing batch effect
BatchEffect DESeq2
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
1
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15
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3.8k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.6 years ago demisa • 0
7
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4
replies
17k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 3.9 years ago by • 0 • written 4.7 years ago by ▴ 20
2
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2
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1.6k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
2
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2
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1.4k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 5.0 years ago by ▴ 360 • written 5.0 years ago by ▴ 10
1
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3
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1.5k
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
0
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1
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1.5k
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
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2
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1.4k
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extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 5.0 years ago by ▴ 90 • written 5.0 years ago by ▴ 120
1
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1
reply
1.6k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 5.0 years ago by ★ 29k • written 5.0 years ago by • 0
1
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1
reply
2.0k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
0
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0
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1.3k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
5.1 years ago hamza_karakurt ▴ 60
2
votes
4
replies
6.1k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
1
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6
replies
2.4k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 120
1
vote
5
replies
1.6k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
4
votes
10
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2.8k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 30
3
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6
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3.4k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 9.1 years ago by ▴ 50 • written 9.1 years ago by ▴ 10
6
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4
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4.6k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 10.4 years ago by ★ 29k • written 10.4 years ago by ▴ 840
3
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6
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3.5k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 10.5 years ago by • 0 • written 11.1 years ago by ▴ 10
2
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3
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3.3k
views
Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 840
1
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5
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2.6k
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Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 10.6 years ago by ▴ 830 • written 10.6 years ago by ▴ 840
2
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1
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1.9k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 10.8 years ago by 53k • written 10.8 years ago by • 0
0
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0
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1.5k
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Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
12.6 years ago Daniel Emden ▴ 10
93 results • Page 2 of 2
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