Showing : batcheffect • reset
2
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4
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1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 10 days ago by 51k • written 14 days ago by • 0
0
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2
replies
413
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
4 weeks ago • updated 29 days ago José • 0
0
votes
6
replies
784
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 26 days ago by 42k • written 6 weeks ago by • 0
5
votes
4
replies
423
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
0
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5
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542
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heatmap with batch effect
DESeq2 BatchEffect
6 weeks ago tothuhien • 0
2
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2
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310
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
8 weeks ago sukeshinik5 ▴ 20
0
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2
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360
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 11 weeks ago by • 0
4
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7
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1.1k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 3 months ago by ▴ 10 • written 4 months ago by ▴ 70
2
votes
2
replies
503
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 5 months ago by ▴ 10 • written 6 months ago by • 0
2
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2
replies
610
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 6 months ago by • 0
0
votes
1
reply
350
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 11 weeks ago by ▴ 20 • written 6 months ago by • 0
0
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2
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886
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 6 months ago by ▴ 20 • written 6 months ago by • 0
2
votes
9
replies
939
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 months ago by 67k • written 7 months ago by • 0
0
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2
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563
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 months ago catv • 0
0
votes
8
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826
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 months ago michelafrancesconi8 • 0
1
vote
3
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647
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
0
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0
replies
360
views
Can I combine collinear variables into a single value
BatchEffect limma
8 months ago Harrsha • 0
2
votes
1
reply
482
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
4
votes
1
reply
963
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 10 months ago by 67k • written 10 months ago by ▴ 20
0
votes
5
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1.2k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 10 months ago by ★ 4.5k • written 10 months ago by • 0
2
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4
replies
1.1k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 11 months ago by 51k • written 11 months ago by • 0
1
vote
4
replies
955
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
12 months ago Wending • 0
0
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4
replies
949
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 months ago by 42k • written 13 months ago by • 0
0
votes
1
reply
647
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
3
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5
replies
1.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
2
votes
5
replies
2.0k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 15 months ago by 51k • written 15 months ago by • 0
2
votes
3
replies
1.9k
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 15 months ago by 67k • written 15 months ago by ▴ 10
3
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4
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1.2k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
15 months ago Eva ▴ 10
0
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2
replies
860
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
16 months ago Eleonora • 0
1
vote
1
reply
617
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 16 months ago by 51k • written 16 months ago by • 0
2
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3
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1.8k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 17 months ago by ★ 4.5k • written 17 months ago by ▴ 10
0
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0
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564
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
17 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
685
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 17 months ago by ★ 4.5k • written 17 months ago by • 0
2
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5
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1.7k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 months ago by • 0 • written 17 months ago by • 0
1
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2
replies
1.4k
views
Batch effect between biological replicates
BatchEffect DESeq2
18 months ago gtechbio ▴ 10
0
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4
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1.3k
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Combine RNA-seq
BatchEffect R rnaseq
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
2
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4
replies
1.9k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
19 months ago vk • 0
2
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2
replies
1.3k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 19 months ago by ★ 4.5k • written 19 months ago by ▴ 30
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 20 months ago by ★ 4.5k • written 20 months ago by ▴ 20
2
votes
1
reply
877
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 15 months ago by • 0 • written 20 months ago by ▴ 200
3
votes
2
replies
1.0k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
20 months ago chf • 0
2
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1
reply
2.3k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
0
votes
1
reply
609
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 21 months ago by 42k • written 21 months ago by • 0
1
vote
1
reply
1.0k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 21 months ago by 67k • written 21 months ago by • 0
5
votes
2
replies
1.0k
views
Sva and batch effect
limma BatchEffect sva
updated 22 months ago by 51k • written 22 months ago by • 0
1
vote
1
reply
2.9k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 22 months ago by ★ 4.5k • written 22 months ago by ▴ 50
0
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0
replies
1.0k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
22 months ago Zhijie • 0
1
vote
0
replies
914
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
23 months ago r_grau ▴ 10
1
vote
2
replies
1.1k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
3
votes
10
replies
2.3k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
2.1 years ago eve.olszanowski • 0
50 results • Page 1 of 1
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Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Answer: HilBertVis install error by James W. MacDonald 67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
Votes
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
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