Showing : batcheffect • reset
1
vote
3
replies
40
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
1 hour ago • updated 6 minutes ago Alexandre • 0
0
votes
2
replies
152
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 days ago • updated 3 days ago catv • 0
0
votes
8
replies
374
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
7 weeks ago • updated 6 weeks ago michelafrancesconi8 • 0
1
vote
3
replies
343
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 weeks ago by ★ 1.3k • written 7 weeks ago by ▴ 10
0
votes
0
replies
142
views
Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
2
votes
1
reply
244
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
0
votes
1
reply
271
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
0
votes
5
replies
518
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
votes
4
replies
609
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
vote
4
replies
606
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
0
votes
4
replies
567
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 days ago by 41k • written 6 months ago by • 0
0
votes
1
reply
434
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
3
votes
5
replies
819
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
2
votes
5
replies
1.3k
views
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
2
votes
3
replies
1.0k
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 8 months ago by 65k • written 8 months ago by ▴ 10
3
votes
4
replies
850
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
votes
2
replies
597
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 months ago Eleonora • 0
1
vote
1
reply
443
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
votes
3
replies
1.1k
views
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 ★ 4.0k • written 10 months ago by ▴ 10
0
votes
0
replies
381
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
483
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 days ago by • 0 • written 10 months ago by • 0
1
vote
2
replies
957
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
0
votes
4
replies
881
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
2
votes
4
replies
1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
2
votes
2
replies
853
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.0k • written 12 months ago by ▴ 30
2
votes
3
replies
872
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
0
votes
1
reply
609
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 13 months ago by ▴ 20
3
votes
2
replies
722
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
13 months ago chf • 0
2
votes
1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
0
votes
1
reply
477
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 14 months ago by 41k • written 14 months ago by • 0
1
vote
1
reply
740
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 14 months ago by 65k • written 14 months ago by • 0
5
votes
2
replies
756
views
Sva and batch effect
limma BatchEffect sva
updated 14 months ago by 50k • written 14 months ago by • 0
1
vote
1
reply
1.6k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 50
0
votes
0
replies
716
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
15 months ago Zhijie • 0
1
vote
0
replies
651
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
1
vote
2
replies
875
views
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
3
votes
10
replies
1.9k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
18 months ago eve.olszanowski • 0
1
vote
2
replies
786
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
18 months ago annamariabugaj ▴ 10
0
votes
1
reply
950
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
0
votes
1
reply
860
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 21 months ago by 50k • written 21 months ago by • 0
1
vote
1
reply
695
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 22 months ago by 41k • written 22 months ago by • 0
6
votes
7
replies
1.8k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
22 months ago lmrogers34 ▴ 10
2
votes
1
reply
1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 23 months ago by 50k • written 23 months ago by ▴ 30
0
votes
1
reply
911
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by ▴ 30
0
votes
0
replies
500
views
Is it possible to do batch correction on Ht-Seq raw counts instead of using normalized counts? What's the difference?
Normalisedcounts Rawcounts Ht-SeqRNAData BatchEffect
2.2 years ago Ety • 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
0
votes
2
replies
1.0k
views
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 2.3 years ago by • 0
0
votes
2
replies
924
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
France, 1 minute ago
France, 2 minutes ago
Germany, 3 minutes ago
France, 5 minutes ago
India, 7 minutes ago
Traffic: 1076 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6