Showing : batcheffect • reset
2
votes
4
replies
1.5k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 2 days ago by 51k • written 6 days ago by • 0
0
votes
2
replies
396
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
23 days ago • updated 21 days ago José • 0
0
votes
6
replies
755
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 18 days ago by 42k • written 5 weeks ago by • 0
5
votes
4
replies
412
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
0
votes
5
replies
506
views
heatmap with batch effect
DESeq2 BatchEffect
5 weeks ago tothuhien • 0
2
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2
replies
300
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
7 weeks ago sukeshinik5 ▴ 20
0
votes
2
replies
350
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 10 weeks ago by • 0
4
votes
7
replies
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
493
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
2
votes
2
replies
599
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
0
votes
1
reply
337
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 9 weeks ago by ▴ 20 • written 6 months ago by • 0
0
votes
2
replies
849
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
923
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
2
replies
553
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 months ago catv • 0
0
votes
8
replies
816
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 months ago michelafrancesconi8 • 0
1
vote
3
replies
637
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
0
votes
0
replies
352
views
Can I combine collinear variables into a single value
BatchEffect limma
8 months ago Harrsha • 0
2
votes
1
reply
475
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
4
votes
1
reply
937
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 9 months ago by 67k • written 9 months ago by ▴ 20
0
votes
5
replies
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
votes
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
939
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
votes
4
replies
936
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 months ago by 42k • written 12 months ago by • 0
0
votes
1
reply
641
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 13 months ago by ★ 4.5k • written 13 months ago by • 0
3
votes
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
votes
4
replies
1.2k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
15 months ago Eva ▴ 10
0
votes
2
replies
847
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
16 months ago Eleonora • 0
1
vote
1
reply
608
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
votes
3
replies
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 16 months ago by ★ 4.5k • written 16 months ago by ▴ 10
0
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0
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558
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
16 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
679
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 16 months ago by ★ 4.5k • written 16 months ago by • 0
2
votes
5
replies
1.6k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 months ago by • 0 • written 17 months ago by • 0
1
vote
2
replies
1.4k
views
Batch effect between biological replicates
BatchEffect DESeq2
18 months ago gtechbio ▴ 10
0
votes
4
replies
1.3k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
2
votes
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
votes
2
replies
1.2k
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
1.2k
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
866
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
votes
1
reply
2.2k
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
602
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 21 months ago by 51k • written 21 months ago by • 0
1
vote
1
reply
2.9k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 21 months ago by ★ 4.5k • written 21 months ago by ▴ 50
0
votes
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
909
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
22 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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Comment: Bioconductor 3.18 is Released! by thelmatertl • 0
This is a release that expresses gratitude to the developers and community members for their contributions and the new features enhance the…
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by daniela.gutierrezandrade • 0
Hello, I am running into a similar issue. After setting the design, at the beginning of the analysis I filter rows with low counts. d…
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for all of your help! I really appreciate it!
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by Gordon Smyth 51k
Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…
Votes
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
biomaRt rnorvegicus_gene_ensembl not available anymore
A: Does edgeR need to specify reference group?
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