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
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4
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11k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.4 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
2.6 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
785
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
views
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 eve.olszanowski • 0
3
votes
6
replies
3.0k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 9.0 years ago by • 0 • written 9.5 years ago by ▴ 10
3
votes
6
replies
2.3k
views
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
765
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
3
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5
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894
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
893
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
2
votes
2
replies
998
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.3 years ago by ★ 4.1k • written 3.3 years ago by • 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 3.5 years ago by ▴ 350 • written 3.5 years ago by ▴ 10
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 15 months ago by ★ 4.1k • written 15 months ago by • 0
2
votes
4
replies
680
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
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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 4 weeks ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
930
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 20
2
votes
2
replies
979
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
910
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 30
2
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4
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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
279
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
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 23 days ago by 65k • written 23 days ago by • 0
2
votes
5
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1.4k
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
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
2
replies
809
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 10
1
vote
4
replies
661
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
2
replies
910
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
1
vote
2
replies
1.0k
views
Batch effect between biological replicates
BatchEffect DESeq2
12 months ago gtechbio ▴ 10
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
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
3
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970
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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
1
reply
713
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
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
1
reply
509
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
0
replies
687
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
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
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
470
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
1
reply
1.8k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 50
1
vote
2
replies
895
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
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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