Showing : Batcheffect • reset
1
vote
0
replies
1.3k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.8 years ago r_grau ▴ 10
1
vote
2
replies
1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
3
votes
10
replies
3.0k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
3.0 years ago eve.olszanowski • 0
1
vote
2
replies
1.2k
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
3.0 years ago annamariabugaj ▴ 10
0
votes
1
reply
1.7k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
1
vote
1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
6
votes
7
replies
3.3k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
3.3 years ago lmrogers34 ▴ 10
2
votes
1
reply
2.0k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 70
0
votes
1
reply
1.8k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
vote
1
reply
2.0k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by ▴ 70
0
votes
0
replies
716
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
3.6 years ago Ety • 0
1
vote
7
replies
2.1k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 10
0
votes
2
replies
1.4k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.8 years ago by ★ 13k • written 3.8 years ago by • 0
0
votes
2
replies
1.5k
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.9 years ago m.glymenaki • 0
6
votes
6
replies
2.3k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
3.9 years ago ary.lech ▴ 10
0
votes
1
reply
1.4k
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 20
2
votes
2
replies
1.6k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
4.0 years ago p.joshi ▴ 40
1
vote
2
replies
1.3k
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
4.0 years ago • updated 3.7 years ago zeegzaag • 0
1
vote
3
replies
3.8k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
2
votes
4
replies
1.7k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.1 years ago by 43k • written 4.3 years ago by • 0
1
vote
5
replies
4.1k
views
Deseq2 - removing batch effect
BatchEffect DESeq2
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
1
vote
15
replies
3.7k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.5 years ago demisa • 0
7
votes
4
replies
17k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 3.8 years ago by • 0 • written 4.6 years ago by ▴ 20
2
votes
2
replies
1.5k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.6 years ago by ★ 5.0k • written 4.7 years ago by • 0
2
votes
2
replies
1.4k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 4.8 years ago by ▴ 360 • written 4.9 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
0
votes
1
reply
1.4k
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
2
replies
1.4k
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 4.9 years ago by ▴ 90 • written 4.9 years ago by ▴ 120
1
vote
1
reply
1.5k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 4.9 years ago by ★ 29k • written 4.9 years ago by • 0
1
vote
1
reply
1.9k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
0
votes
0
replies
1.2k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.9 years ago hamza_karakurt ▴ 60
2
votes
4
replies
6.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
1
vote
6
replies
2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 120
1
vote
5
replies
1.5k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
4
votes
10
replies
2.7k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 8.4 years ago by 53k • written 8.4 years ago by ▴ 30
3
votes
6
replies
3.3k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 9.0 years ago by ▴ 50 • written 9.0 years ago by ▴ 10
6
votes
4
replies
4.5k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 840
3
votes
6
replies
3.4k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 10.3 years ago by • 0 • written 10.9 years ago by ▴ 10
2
votes
3
replies
3.3k
views
Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 840
1
vote
5
replies
2.5k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 10.5 years ago by ▴ 830 • written 10.5 years ago by ▴ 840
2
votes
1
reply
1.9k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 10.7 years ago by 53k • written 10.7 years ago by • 0
0
votes
0
replies
1.5k
views
Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
12.5 years ago Daniel Emden ▴ 10
93 results • Page 2 of 2
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Locations • All
Seattle, WA, United States, 29 minutes ago
United States, 38 minutes ago
UK/Cambridge, 40 minutes ago
San Diego, 1 hour ago
Denmark, 1 hour ago
Traffic: 735 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