Showing : batcheffect • reset
2
votes
2
replies
225
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 days ago by • 0 • written 24 days ago by • 0
2
votes
2
replies
355
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 days ago by • 0 • written 24 days ago by • 0
0
votes
0
replies
103
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
28 days ago Shaimaa Gamal • 0
0
votes
2
replies
241
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 4 weeks ago by ▴ 10 • written 4 weeks ago by • 0
2
votes
9
replies
487
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
votes
2
replies
286
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 weeks ago catv • 0
0
votes
8
replies
501
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
3 months ago michelafrancesconi8 • 0
1
vote
3
replies
434
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 3 months ago by ★ 1.4k • written 3 months ago by ▴ 10
0
votes
0
replies
194
views
Can I combine collinear variables into a single value
BatchEffect limma
3 months ago Harrsha • 0
2
votes
1
reply
310
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
4
votes
1
reply
468
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 4 months ago by 66k • written 4 months ago by ▴ 20
0
votes
5
replies
659
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
2
votes
4
replies
735
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 6 months ago by 51k • written 6 months ago by • 0
1
vote
4
replies
698
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
7 months ago Wending • 0
0
votes
4
replies
665
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 weeks ago by 42k • written 7 months ago by • 0
0
votes
1
reply
496
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
3
votes
5
replies
971
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 9 months ago by ★ 4.2k • written 9 months ago by • 0
2
votes
5
replies
1.5k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 10 months ago by 51k • written 10 months ago by • 0
2
votes
3
replies
1.3k
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 10 months ago by 66k • written 10 months ago by ▴ 10
3
votes
4
replies
929
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
10 months ago Eva ▴ 10
0
votes
2
replies
683
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
11 months ago • updated 10 months ago Eleonora • 0
1
vote
1
reply
483
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 11 months ago by 51k • written 11 months ago by • 0
2
votes
3
replies
1.3k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
0
votes
0
replies
425
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
11 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
524
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 11 months ago by ★ 4.2k • written 11 months ago by • 0
2
votes
5
replies
1.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 weeks ago by • 0 • written 12 months ago by • 0
1
vote
2
replies
1.0k
views
Batch effect between biological replicates
BatchEffect DESeq2
13 months ago gtechbio ▴ 10
0
votes
4
replies
962
views
Combine RNA-seq
BatchEffect R rnaseq
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
2
votes
4
replies
1.6k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
14 months ago vk • 0
2
votes
2
replies
965
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 14 months ago by ★ 4.2k • written 14 months ago by ▴ 30
2
votes
3
replies
982
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 15 months ago by ▴ 20
0
votes
1
reply
653
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 9 months ago by • 0 • written 15 months ago by ▴ 20
3
votes
2
replies
810
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
15 months ago chf • 0
2
votes
1
reply
1.6k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
0
votes
1
reply
506
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 15 months ago by 42k • written 16 months ago by • 0
1
vote
1
reply
804
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 16 months ago by 66k • written 16 months ago by • 0
5
votes
2
replies
821
views
Sva and batch effect
limma BatchEffect sva
updated 16 months ago by 51k • written 16 months ago by • 0
1
vote
1
reply
1.9k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 16 months ago by ★ 4.2k • written 16 months ago by ▴ 50
0
votes
0
replies
789
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
17 months ago Zhijie • 0
1
vote
0
replies
726
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
17 months ago r_grau ▴ 10
1
vote
2
replies
944
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
3
votes
10
replies
2.0k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
20 months ago eve.olszanowski • 0
1
vote
2
replies
827
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
20 months ago annamariabugaj ▴ 10
0
votes
1
reply
1.0k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 21 months ago by 42k • written 22 months ago by • 0
0
votes
1
reply
913
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 22 months ago by 51k • written 22 months ago by • 0
1
vote
1
reply
735
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
6
votes
7
replies
2.0k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
2.0 years ago • updated 24 months ago lmrogers34 ▴ 10
2
votes
1
reply
1.4k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 2.0 years ago by 51k • written 2.0 years ago by ▴ 50
0
votes
1
reply
996
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
1
vote
1
reply
1.2k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.3 years ago by ★ 4.2k • written 2.3 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Votes
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
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