Showing : Batch • reset
4
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1
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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
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7
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1.7k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.9 years ago by 67k • written 2.9 years ago by ▴ 10
0
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2
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1.2k
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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
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7
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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
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1
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1.2k
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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
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5
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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
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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
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8
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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
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2
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920
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DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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3
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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
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1
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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
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3
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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
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6
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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
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20
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22k
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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
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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
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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
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3
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1.1k
views
DESEQ2 Batch effect
deseq2 batch
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
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3
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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
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4
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2.9k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
8.1 years ago j.viana • 0
2
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1
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1.3k
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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
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Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
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
@[sandtrix][1] This is useful information. [1]: https://sandtrix.io
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…
Votes
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
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
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