Showing : BatchEffect • reset
2
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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 9 months ago by 50k • written 9 months ago by • 0
6
votes
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
0
votes
4
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914
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
3
votes
6
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3.0k
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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
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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 7.6 years ago by ▴ 50 • written 7.6 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
1
vote
5
replies
1.1k
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 10
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
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
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
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
0
votes
2
replies
934
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by ▴ 120
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
0
votes
2
replies
953
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
2
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4
replies
1.5k
views
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
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
2
votes
3
replies
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
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 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 830
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
0
votes
1
reply
881
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
2
replies
754
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
0
votes
1
reply
327
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
1
reply
271
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
6
votes
7
replies
1.9k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
23 months ago lmrogers34 ▴ 10
0
votes
8
replies
431
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 weeks ago michelafrancesconi8 • 0
1
vote
2
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803
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 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
501
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
votes
9
replies
406
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 16 days ago by 65k • written 17 days ago by • 0
1
vote
2
replies
900
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
3
votes
5
replies
877
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
457
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
6
votes
4
replies
11k
views
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
0
votes
2
replies
1.0k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.4 years ago by ★ 13k • written 2.4 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
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
0
votes
2
replies
632
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
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
1
vote
3
replies
376
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by ▴ 10
5
votes
2
replies
779
views
Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
2
votes
4
replies
661
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
1
vote
1
reply
760
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
844
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 2.6 years ago by 65k • written 2.6 years ago by ▴ 20
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
0
votes
1
reply
487
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 42k • written 15 months ago by • 0
0
votes
5
replies
591
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
2
replies
985
views
Batch effect between biological replicates
BatchEffect DESeq2
12 months ago gtechbio ▴ 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
50 results • Page 1 of 1
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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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thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
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Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
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did you find a solution? I´m having the same problem
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