Showing : RUVSeq • reset
2
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2
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578
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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
637
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 7 months ago by 43k • written 8 months ago by • 0
1
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0
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361
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
8 months ago Erdi ▴ 10
0
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0
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354
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determine k during RUVSeq
RUVSeq RUVnormalize
9 months ago Ειρήνη • 0
2
votes
9
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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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673
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
13 months ago Shaimaa Gamal • 0
4
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3
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850
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 13 months ago by 52k • written 13 months ago by • 0
2
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3
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781
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 13 months ago by 68k • written 13 months ago by • 0
2
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5
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986
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
13 months ago ctlong • 0
0
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6
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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
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9
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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 18 months ago by ★ 4.7k • written 18 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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1.3k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
23 months ago AZ ▴ 30
0
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0
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609
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
23 months ago Luca • 0
1
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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
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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
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3
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1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
0
votes
0
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686
views
RUVg for SNAP-ChIP ?
RUVSeq
2.3 years ago Bogdan ▴ 670
0
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1
reply
905
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 2.8 years ago by ▴ 50
1
vote
1
reply
984
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
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2.1k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.8 years ago Jess • 0
0
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5
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5.1k
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 4.0 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
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2.2k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 7 months ago by ▴ 70 • written 3.7 years ago by ▴ 50
2
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6
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5.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.7 years ago reganhayward • 0
2
votes
2
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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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828
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.0 years ago bioinfc • 0
0
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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
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2.0k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 20
0
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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
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24k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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0
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841
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.8 years ago acquaviva.massimo • 0
2
votes
6
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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
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4
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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
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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
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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
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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
914
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
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0
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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
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2.9k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.8 years ago by ▴ 980 • written 5.9 years ago by • 0
2
votes
4
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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
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3
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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 6.1 years ago by ▴ 680
50 results • Page 1 of 1
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Answer: library org.Hs.eg.db failing to install by James W. MacDonald 68k
It should just install. ``` > library(BiocManager) Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14 ucrt) W…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Thank you so much for your quick reply! I was worried if some underlying technical artifact or unusual behavior would be causing the patter…
Answer: Surprising behavior for DEXseq dispersion estimate plot? by Michael Love 43k
The red points are just slowly moving toward -Inf. They tend to have variance < mean (if it were a simple design and you could just look at…
Answer: DESeq use in lipidomic analysis by Michael Love 43k
I would go for limma rather than a NB-based method. See the papers on limma for metabolomics / proteomics.
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[FFH4X][1] Injector is a Free Fire mod menu software that includes a variety of intriguing hack features such as aimbot, auto headshot, fly…
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Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Calculating TOM in blockwise WGCNA
A: What is the "linear model" part used for in Limma?
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