Showing : BatchEffect • reset
2
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4
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1.6k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 5 weeks ago by 52k • written 6 weeks ago by • 0
0
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2
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485
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
8 weeks ago José • 0
0
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6
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838
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
5
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4
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465
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
0
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5
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633
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heatmap with batch effect
DESeq2 BatchEffect
11 weeks ago • updated 10 weeks ago tothuhien • 0
2
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2
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347
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
12 weeks ago sukeshinik5 ▴ 20
0
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2
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398
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 3 months ago by • 0
4
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7
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1.2k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 4 months ago by ▴ 10 • written 5 months ago by ▴ 70
2
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2
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535
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 6 months ago by ▴ 10 • written 7 months ago by • 0
2
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2
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638
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 6 months ago by ▴ 10 • written 7 months ago by • 0
0
votes
1
reply
372
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 3 months ago by ▴ 20 • written 7 months ago by • 0
0
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2
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989
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 7 months ago by ▴ 20 • written 7 months ago by • 0
2
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9
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999
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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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603
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 months ago catv • 0
0
votes
8
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872
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 months ago michelafrancesconi8 • 0
1
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3
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694
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
0
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0
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381
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Can I combine collinear variables into a single value
BatchEffect limma
9 months ago Harrsha • 0
2
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1
reply
499
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
4
votes
1
reply
1.0k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 11 months ago by 67k • written 11 months ago by ▴ 20
0
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5
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1.3k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
2
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4
replies
1.2k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 12 months ago by 52k • written 12 months ago by • 0
1
vote
4
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984
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
13 months ago Wending • 0
0
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4
replies
981
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 months ago by 43k • written 14 months ago by • 0
0
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1
reply
658
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
3
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5
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1.5k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
2
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5
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2.1k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 16 months ago by 52k • written 16 months ago by • 0
2
votes
3
replies
2.0k
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 16 months ago by 67k • written 16 months ago by ▴ 10
3
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4
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1.3k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
16 months ago Eva ▴ 10
0
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2
replies
883
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
17 months ago Eleonora • 0
1
vote
1
reply
632
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 17 months ago by 52k • written 17 months ago by • 0
2
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3
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1.9k
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 ★ 4.6k • written 18 months ago by ▴ 10
0
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0
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583
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
18 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
700
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
2
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5
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1.7k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 months ago by • 0 • written 18 months ago by • 0
1
vote
2
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1.4k
views
Batch effect between biological replicates
BatchEffect DESeq2
19 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 20 months ago by ★ 1.4k • written 20 months ago by • 0
2
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4
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2.0k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
20 months ago vk • 0
2
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2
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1.3k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 20 months ago by ★ 4.6k • written 20 months ago by ▴ 30
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 20
2
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1
reply
905
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 16 months ago by • 0 • written 21 months ago by ▴ 200
3
votes
2
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1.1k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
21 months ago chf • 0
2
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1
reply
2.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
0
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1
reply
621
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 22 months ago by 43k • written 22 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 22 months ago by 67k • written 22 months ago by • 0
5
votes
2
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1.1k
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Sva and batch effect
limma BatchEffect sva
updated 22 months ago by 52k • written 22 months ago by • 0
1
vote
1
reply
3.1k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 23 months ago by ★ 4.6k • written 23 months ago by ▴ 50
0
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0
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1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
23 months ago Zhijie • 0
1
vote
0
replies
938
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
24 months ago r_grau ▴ 10
1
vote
2
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1.2k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
3
votes
10
replies
2.4k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
2.2 years ago eve.olszanowski • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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