Showing : ruvseq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 8 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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1
reply
247
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
0
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3
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407
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
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1
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1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 8 months ago by 43k • written 9 months ago by • 0
2
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2
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926
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
17 months ago BioinfGuru ▴ 70
0
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1
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1.1k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 18 months ago by 43k • written 18 months ago by • 0
1
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0
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641
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
18 months ago Erdi ▴ 10
0
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0
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580
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determine k during RUVSeq
RUVSeq RUVnormalize
20 months ago Ειρήνη • 0
2
votes
9
replies
1.9k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 20 months ago by 68k • written 20 months ago by • 0
3
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6
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1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
21 months ago nhaus ▴ 70
3
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2
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1.1k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago Shaimaa Gamal • 0
4
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3
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1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
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5
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1.5k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
2.0 years ago ctlong • 0
0
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6
replies
1.5k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 21 months ago by 53k • written 2.3 years ago by ▴ 10
3
votes
5
replies
2.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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4
replies
1.4k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.5 years ago • updated 2.4 years ago anne.hoffrichter • 0
3
votes
12
replies
3.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.8 years ago AZ ▴ 20
0
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0
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792
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.8 years ago Luca • 0
1
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2
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1.9k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.8 years ago garbuzov • 0
3
votes
6
replies
2.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
3.0 years ago • updated 2.8 years ago Zainab ▴ 20
0
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1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 10
0
votes
3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
0
replies
851
views
RUVg for SNAP-ChIP ?
RUVSeq
3.1 years ago Bogdan ▴ 670
0
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1
reply
1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.5 years ago Tongjun • 0
0
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4
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3.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.6 years ago Mohamed ▴ 30
1
vote
7
replies
2.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 60
1
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1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 20
2
votes
7
replies
2.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.7 years ago • updated 3.6 years ago Jess • 0
0
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5
replies
6.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.0 years ago by ★ 5.0k • written 4.8 years ago by • 0
1
vote
1
reply
1.4k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.3 years ago • updated 4.2 years ago Mallory ▴ 10
1
vote
5
replies
2.7k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 17 months ago by ▴ 70 • written 4.6 years ago by ▴ 60
2
votes
6
replies
6.2k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.6 years ago reganhayward • 0
2
votes
2
replies
2.2k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.7 years ago elizabethe819 • 0
0
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0
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1.0k
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.8 years ago bioinfc • 0
0
votes
7
replies
2.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.9 years ago by ▴ 980 • written 4.9 years ago by • 0
5
votes
6
replies
2.5k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 20
0
votes
2
replies
2.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
0
replies
1.0k
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.7 years ago acquaviva.massimo • 0
2
votes
6
replies
2.1k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
2
votes
4
replies
3.2k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
3
replies
1.6k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
4
replies
3.2k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.2 years ago Arindam ▴ 80
0
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2
replies
2.4k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.3 years ago by ▴ 980 • written 6.3 years ago by • 0
1
vote
1
reply
1.9k
views
Using RUVs with known batches
ruvseq deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
0
replies
1.3k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.6 years ago garbuzov • 0
108 results • Page 1 of 3
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Replies
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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