Showing : batch • reset
4
votes
1
reply
1.6k
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 23 months ago by ★ 4.6k • written 23 months ago by ▴ 50
0
votes
1
reply
1.4k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
1
vote
7
replies
1.7k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.9 years ago by 67k • written 2.9 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.0 years ago by ★ 13k • written 3.0 years ago by • 0
5
votes
7
replies
3.9k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 4.1 years ago by • 0 • written 5.4 years ago by • 0
0
votes
1
reply
1.2k
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
votes
5
replies
2.2k
views
DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 50
1
vote
4
replies
2.2k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 4.3 years ago by ▴ 980 • written 4.3 years ago by ★ 1.5k
2
votes
8
replies
5.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.4 years ago Pietro ▴ 40
0
votes
2
replies
919
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
3
replies
1.2k
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
0
votes
1
reply
1.4k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
3
votes
3
replies
1.2k
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
6
votes
6
replies
1.9k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 20
10
votes
20
replies
22k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 12 weeks ago by 67k • written 5.6 years ago by ▴ 30
0
votes
1
reply
929
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
3
votes
5
replies
1.7k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
0
votes
3
replies
1.1k
views
DESEQ2 Batch effect
deseq2 batch
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
3
replies
1.1k
views
Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
0
votes
4
replies
2.9k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
8.1 years ago j.viana • 0
2
votes
1
reply
1.3k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq edgeR limma removebatcheffect() batch
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 80
21 results • Page 1 of 1
Recent ...
Replies
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Comment: Packages don't update, but no error or warning is thrown by neighsanlo • 0
This is useful information.
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by freemanmclaughlin9969289 • 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Comment: How to get around the warning message: mzR has been built against a different Rc by Nan • 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
Awards • All
Teacher to dsull ▴ 40
Popular Question to bpshtiwan ▴ 10
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Locations • All
UPF, Barcelona, Spain, 59 minutes ago
China, 1 hour ago
Vietnam, 4 hours ago
Türkiye, 4 hours ago
The city by the bay, 5 hours ago
Traffic: 616 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