Showing : BatchEffect • reset
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.1 years ago demisa • 0
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
3
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10
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1.9k
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
19 months ago • updated 18 months ago eve.olszanowski • 0
2
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9
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392
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 11 days ago by • 0
0
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8
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406
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
8 weeks ago michelafrancesconi8 • 0
6
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7
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1.8k
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Batch effect with one sample being in two batches
BatchEffect DESeq2
23 months ago • updated 22 months ago lmrogers34 ▴ 10
1
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7
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1.3k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
6
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6
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1.4k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
3
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6
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2.3k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 7.5 years ago by ▴ 50 • written 7.5 years ago by ▴ 10
1
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6
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1.7k
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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
3
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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
1
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5
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1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 9.0 years ago by ▴ 830 • written 9.1 years ago by ▴ 830
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 days ago by • 0 • written 10 months ago by • 0
0
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5
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568
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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
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5
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1.1k
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
2
votes
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 8 months ago by 50k • written 8 months ago by • 0
3
votes
5
replies
860
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
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5
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2.7k
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Deseq2 - removing batch effect
BatchEffect DESeq2
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
0
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4
replies
602
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 days ago by 41k • written 6 months ago by • 0
2
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4
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1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
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 2.3 years ago by • 0 • written 3.2 years ago by ▴ 10
3
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4
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876
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
2
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4
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1.2k
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 41k • written 2.9 years ago by • 0
0
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4
replies
905
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
2
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4
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4.9k
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
6
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4
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4.0k
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
2
votes
4
replies
635
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
1
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4
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636
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
2
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3
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1.1k
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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
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3
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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
1
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3
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954
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Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.4 years ago by 50k • written 3.5 years ago by • 0
1
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3
replies
365
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
2
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3
replies
1.1k
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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
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3
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2.3k
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Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
2
votes
3
replies
895
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
1
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2
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795
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
19 months ago annamariabugaj ▴ 10
2
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2
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986
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
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2
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213
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
17 days ago • updated 14 days ago catv • 0
1
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2
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884
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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
2
votes
2
replies
882
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
1
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2
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980
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Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
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2
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943
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
2
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2
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1.0k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 3.4 years ago by ▴ 350 • written 3.4 years ago by ▴ 10
0
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2
replies
1.0k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.3 years ago by ★ 13k • written 2.4 years ago by • 0
5
votes
2
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769
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Sva and batch effect
limma BatchEffect sva
updated 15 months ago by 50k • written 15 months ago by • 0
3
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2
replies
746
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
0
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2
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623
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
2
replies
895
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.3k • written 18 months ago by • 0
0
votes
2
replies
931
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
968
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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
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset) by Caio • 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by gene_bioconductor ▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Votes
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
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