Showing : Batch • reset
10
votes
18
replies
16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
4.9 years ago Mozart ▴ 30
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
4
votes
7
replies
3.4k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 3.4 years ago by • 0 • written 4.7 years ago by • 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
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
0
votes
5
replies
1.7k
views
DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
0
votes
4
replies
2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.4 years ago j.viana • 0
1
vote
4
replies
1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 3.6 years ago by ▴ 950 • written 3.6 years ago by ★ 1.5k
3
votes
3
replies
976
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
3
votes
3
replies
931
views
Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 30
0
votes
3
replies
952
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
votes
3
replies
940
views
DESEQ2 Batch effect
deseq2 batch
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
2
replies
678
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
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
1
reply
948
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
768
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
0
votes
1
reply
936
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
4
votes
1
reply
1.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 50
2
votes
1
reply
1.1k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq edgeR limma removebatcheffect() batch
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 80
21 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
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?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
Germany, 1 minute ago
France, 11 minutes ago
France, 17 minutes ago
France, 22 minutes ago
Germany, 28 minutes ago
Traffic: 971 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