Showing : RUVSeq • reset
2
votes
2
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573
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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
6 months ago BioinfGuru ▴ 70
0
votes
1
reply
623
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 7 months ago by 43k • written 7 months ago by • 0
1
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0
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353
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
7 months ago Erdi ▴ 10
0
votes
0
replies
350
views
determine k during RUVSeq
RUVSeq RUVnormalize
9 months ago Ειρήνη • 0
2
votes
9
replies
1.2k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 months ago by 68k • written 10 months ago by • 0
3
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6
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1.1k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
10 months ago nhaus ▴ 70
3
votes
2
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666
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 months ago Shaimaa Gamal • 0
4
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3
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841
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 months ago by 52k • written 12 months ago by • 0
2
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3
replies
772
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 months ago by 68k • written 12 months ago by • 0
2
votes
5
replies
957
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
13 months ago ctlong • 0
0
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6
replies
1.1k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 15 months ago by 43k • written 16 months ago by • 0
5
votes
9
replies
2.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 10 months ago by 52k • written 17 months ago by ▴ 10
3
votes
5
replies
1.7k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 17 months ago by ★ 4.7k • written 17 months ago by • 0
0
votes
4
replies
1.1k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
19 months ago anne.hoffrichter • 0
3
votes
12
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2.3k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
1
vote
2
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1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
22 months ago AZ ▴ 30
0
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0
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601
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
23 months ago Luca • 0
1
vote
2
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1.5k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
23 months ago garbuzov • 0
3
votes
6
replies
1.5k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.1 years ago • updated 23 months ago Zainab ▴ 20
0
votes
1
reply
1.0k
views
RUV with K more than 1.
RUVSeq
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by ▴ 10
0
votes
3
replies
1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
0
replies
681
views
RUVg for SNAP-ChIP ?
RUVSeq
2.2 years ago Bogdan ▴ 670
0
votes
1
reply
901
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.6 years ago Tongjun • 0
0
votes
4
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3.1k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.7 years ago Mohamed ▴ 30
1
vote
7
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2.1k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 50
1
vote
1
reply
981
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 20
2
votes
7
replies
2.1k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.8 years ago Jess • 0
0
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5
replies
5.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.1 years ago by ★ 4.7k • written 3.9 years ago by • 0
1
vote
1
reply
1.1k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.4 years ago • updated 3.3 years ago Mallory ▴ 10
1
vote
5
replies
2.2k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 6 months ago by ▴ 70 • written 3.7 years ago by ▴ 50
2
votes
6
replies
5.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.7 years ago reganhayward • 0
2
votes
2
replies
1.8k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.8 years ago elizabethe819 • 0
0
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0
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819
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.9 years ago bioinfc • 0
0
votes
7
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2.1k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.1 years ago by ▴ 980 • written 4.1 years ago by • 0
5
votes
6
replies
2.0k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 20
0
votes
2
replies
1.7k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
0
replies
832
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.8 years ago acquaviva.massimo • 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
2
votes
4
replies
2.5k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
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3
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1.2k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1
vote
4
replies
2.7k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.3 years ago Arindam ▴ 80
0
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2
replies
2.0k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.4 years ago by ▴ 980 • written 5.4 years ago by • 0
1
vote
1
reply
1.6k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
0
votes
1
reply
912
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
0
replies
1.1k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.7 years ago garbuzov • 0
0
votes
2
replies
2.9k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.7 years ago by ▴ 980 • written 5.9 years ago by • 0
2
votes
4
replies
2.8k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.8 years ago by ▴ 980 • written 5.8 years ago by ▴ 260
0
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0
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1.0k
views
RUVseq: Use of known controls with RUVg
RUVseq
5.8 years ago bio.erikson • 0
1
vote
3
replies
2.7k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 6.0 years ago by 52k • written 6.0 years ago by ▴ 680
50 results • Page 1 of 1
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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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