Showing : RUVSeq • reset
2
votes
2
replies
465
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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
3 months ago BioinfGuru ▴ 70
0
votes
1
reply
441
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 4 months ago by 42k • written 4 months ago by • 0
1
vote
0
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271
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
4 months ago Erdi ▴ 10
0
votes
0
replies
258
views
determine k during RUVSeq
RUVSeq RUVnormalize
6 months ago Ειρήνη • 0
2
votes
9
replies
931
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 months ago by 67k • written 6 months ago by • 0
3
votes
6
replies
819
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
7 months ago nhaus ▴ 70
3
votes
2
replies
559
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
9 months ago Shaimaa Gamal • 0
4
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3
replies
680
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 9 months ago by 51k • written 9 months ago by • 0
2
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3
replies
654
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 9 months ago by 67k • written 9 months ago by • 0
2
votes
5
replies
780
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
10 months ago ctlong • 0
0
votes
6
replies
959
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 12 months ago by 42k • written 12 months ago by • 0
5
votes
9
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1.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 7 months ago by 51k • written 13 months ago by ▴ 10
3
votes
5
replies
1.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
0
votes
4
replies
945
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
15 months ago anne.hoffrichter • 0
3
votes
12
replies
2.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 19 months ago by 42k • written 19 months ago by ▴ 10
1
vote
2
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1.1k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
19 months ago AZ ▴ 30
0
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0
replies
539
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
19 months ago Luca • 0
1
vote
2
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1.3k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
20 months ago garbuzov • 0
3
votes
6
replies
1.4k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
21 months ago • updated 20 months ago Zainab ▴ 20
0
votes
1
reply
906
views
RUV with K more than 1.
RUVSeq
updated 22 months ago by ★ 4.5k • written 22 months ago by ▴ 10
0
votes
3
replies
1.2k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 23 months ago by 42k • written 23 months ago by • 0
0
votes
0
replies
629
views
RUVg for SNAP-ChIP ?
RUVSeq
23 months ago Bogdan ▴ 670
0
votes
1
reply
827
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.3 years ago Tongjun • 0
0
votes
4
replies
2.7k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.4 years ago Mohamed ▴ 30
1
vote
7
replies
1.9k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.4 years ago by 42k • written 2.5 years ago by ▴ 50
1
vote
1
reply
906
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 20
2
votes
7
replies
1.9k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.5 years ago Jess • 0
0
votes
5
replies
4.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.8 years ago by ★ 4.5k • written 3.7 years ago by • 0
1
vote
1
reply
970
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.1 years ago • updated 3.0 years ago Mallory ▴ 10
1
vote
5
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2.0k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 3 months ago by ▴ 70 • written 3.4 years ago by ▴ 50
2
votes
6
replies
5.3k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.4 years ago reganhayward • 0
2
votes
2
replies
1.6k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.5 years ago elizabethe819 • 0
0
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0
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768
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.6 years ago bioinfc • 0
0
votes
7
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1.9k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.8 years ago by ▴ 980 • written 3.8 years ago by • 0
5
votes
6
replies
1.9k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 20
0
votes
2
replies
1.6k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
0
votes
0
replies
761
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.5 years ago acquaviva.massimo • 0
2
votes
6
replies
1.6k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.5 years ago by 51k • written 4.5 years ago by • 0
2
votes
4
replies
2.2k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
3
replies
1.1k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
1
vote
4
replies
2.6k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.0 years ago Arindam ▴ 80
0
votes
2
replies
1.8k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.1 years ago by ▴ 980 • written 5.1 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.3 years ago by 42k • written 5.3 years ago by ▴ 30
0
votes
1
reply
855
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
0
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0
replies
1.0k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.4 years ago garbuzov • 0
0
votes
2
replies
2.8k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.5 years ago by ▴ 980 • written 5.6 years ago by • 0
2
votes
4
replies
2.6k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.5 years ago by ▴ 980 • written 5.5 years ago by ▴ 260
0
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0
replies
946
views
RUVseq: Use of known controls with RUVg
RUVseq
5.5 years ago bio.erikson • 0
1
vote
3
replies
2.5k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.7 years ago by 51k • written 5.8 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: [How to construct a model.matrix ] by kyj2226 • 0
Thanks to you, I learn a lot. Many thanks, Yujin.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Votes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
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