Showing : BatchEffect • reset
0
votes
2
replies
260
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 18 days ago by • 0
4
votes
7
replies
922
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 6 weeks ago by ▴ 10 • written 11 weeks ago by ▴ 70
2
votes
2
replies
437
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 3 months ago by ▴ 10 • written 4 months ago by • 0
2
votes
2
replies
543
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 3 months ago by ▴ 10 • written 4 months ago by • 0
0
votes
1
reply
277
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 15 days ago by ▴ 20 • written 4 months ago by • 0
0
votes
2
replies
619
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 4 months ago by ▴ 20 • written 4 months ago by • 0
2
votes
9
replies
791
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 months ago by 67k • written 4 months ago by • 0
0
votes
2
replies
461
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 months ago catv • 0
0
votes
8
replies
726
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 months ago michelafrancesconi8 • 0
1
vote
3
replies
573
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 10
0
votes
0
replies
308
views
Can I combine collinear variables into a single value
BatchEffect limma
6 months ago Harrsha • 0
2
votes
1
reply
426
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 6 months ago by 42k • written 6 months ago by ▴ 10
4
votes
1
reply
758
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 7 months ago by 67k • written 7 months ago by ▴ 20
0
votes
5
replies
1.0k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 8 months ago by ★ 4.4k • written 8 months ago by • 0
2
votes
4
replies
975
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 9 months ago by 51k • written 9 months ago by • 0
1
vote
4
replies
860
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
10 months ago Wending • 0
0
votes
4
replies
853
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 5 months ago by 42k • written 11 months ago by • 0
0
votes
1
reply
601
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 11 months ago by ★ 4.4k • written 11 months ago by • 0
3
votes
5
replies
1.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 12 months ago by ★ 4.4k • written 12 months ago by • 0
2
votes
5
replies
1.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 13 months ago by 51k • written 13 months ago by • 0
2
votes
3
replies
1.7k
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 13 months ago by 67k • written 13 months ago by ▴ 10
3
votes
4
replies
1.1k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
13 months ago Eva ▴ 10
0
votes
2
replies
796
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
14 months ago Eleonora • 0
1
vote
1
reply
569
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 14 months ago by 51k • written 14 months ago by • 0
2
votes
3
replies
1.7k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 14 months ago by ★ 4.4k • written 14 months ago by ▴ 10
0
votes
0
replies
511
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
14 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
635
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 15 months ago by ★ 4.4k • written 15 months ago by • 0
2
votes
5
replies
1.6k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 5 months ago by • 0 • written 15 months ago by • 0
1
vote
2
replies
1.2k
views
Batch effect between biological replicates
BatchEffect DESeq2
16 months ago gtechbio ▴ 10
0
votes
4
replies
1.2k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
votes
4
replies
1.8k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
17 months ago vk • 0
2
votes
2
replies
1.1k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 17 months ago by ★ 4.4k • written 17 months ago by ▴ 30
2
votes
3
replies
1.2k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 18 months ago by ★ 4.4k • written 18 months ago by ▴ 20
2
votes
1
reply
792
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 13 months ago by • 0 • written 18 months ago by ▴ 200
3
votes
2
replies
966
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
18 months ago chf • 0
2
votes
1
reply
2.0k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 19 months ago by ★ 4.4k • written 19 months ago by • 0
0
votes
1
reply
577
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 19 months ago by 42k • written 19 months ago by • 0
1
vote
1
reply
948
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 19 months ago by 67k • written 19 months ago by • 0
5
votes
2
replies
971
views
Sva and batch effect
limma BatchEffect sva
updated 19 months ago by 51k • written 19 months ago by • 0
1
vote
1
reply
2.5k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 19 months ago by ★ 4.4k • written 19 months ago by ▴ 50
0
votes
0
replies
962
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
20 months ago Zhijie • 0
1
vote
0
replies
849
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
21 months ago r_grau ▴ 10
1
vote
2
replies
1.1k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
3
votes
10
replies
2.2k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
23 months ago eve.olszanowski • 0
1
vote
2
replies
936
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
23 months ago annamariabugaj ▴ 10
0
votes
1
reply
1.3k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
0
votes
1
reply
1.0k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
1
vote
1
reply
851
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
6
votes
7
replies
2.2k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
2.3 years ago • updated 2.2 years ago lmrogers34 ▴ 10
2
votes
1
reply
1.6k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 2.3 years ago by 51k • written 2.3 years ago by ▴ 70
50 results • Page 1 of 1
Recent ...
Replies
Comment: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1 by Gordon Smyth 51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working by James W. MacDonald 67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome by James W. MacDonald 67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
Votes
Comment: AffylmGUI does not start wit R 4.4.1
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
Awards • All
Popular Question to Gordon Smyth 51k
Popular Question to Jose Guillen ▴ 10
Popular Question to micolak0115 • 0
Scholar to Aidan ▴ 40
Popular Question to hayleyw • 0
Locations • All
WEHI, Melbourne, Australia, 5 minutes ago
France, 8 minutes ago
United Kingdom, 11 minutes ago
Australia, 1 hour ago
European Union, 2 hours ago
Traffic: 491 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