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
7.5 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
981
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
942
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
961
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
956
views
DESEQ2 Batch effect
deseq2 batch
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
2
replies
685
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
969
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
773
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
943
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 ★ 4.1k • 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
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
Sweden, 17 minutes ago
France, 20 minutes ago
United Kingdom, 1 hour ago
India, 2 hours ago
The city by the bay, 3 hours ago
Traffic: 511 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