Showing : RUVseq • reset
2
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2
replies
518
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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
4 months ago BioinfGuru ▴ 70
0
votes
1
reply
518
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 5 months ago by 43k • written 6 months ago by • 0
1
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0
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306
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
6 months ago Erdi ▴ 10
0
votes
0
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295
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determine k during RUVSeq
RUVSeq RUVnormalize
7 months ago Ειρήνη • 0
2
votes
9
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1.0k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 months ago by 67k • written 8 months ago by • 0
3
votes
6
replies
913
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 months ago nhaus ▴ 70
3
votes
2
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609
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 months ago Shaimaa Gamal • 0
4
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3
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762
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
2
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3
replies
709
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 0
2
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5
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848
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
11 months ago ctlong • 0
0
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6
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1.0k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 13 months ago by 43k • written 14 months ago by • 0
5
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9
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2.0k
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Batch correction and repeated measures
RUVSeq sva limma
updated 8 months ago by 52k • written 15 months ago by ▴ 10
3
votes
5
replies
1.5k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 15 months ago by ★ 4.6k • written 16 months ago by • 0
0
votes
4
replies
993
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
17 months ago anne.hoffrichter • 0
3
votes
12
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2.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
1
vote
2
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1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
21 months ago AZ ▴ 30
0
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0
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567
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
21 months ago Luca • 0
1
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2
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1.4k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
21 months ago garbuzov • 0
3
votes
6
replies
1.4k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
23 months ago • updated 21 months ago Zainab ▴ 20
0
votes
1
reply
951
views
RUV with K more than 1.
RUVSeq
updated 23 months ago by ★ 4.6k • written 23 months ago by ▴ 10
0
votes
3
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1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
0
replies
648
views
RUVg for SNAP-ChIP ?
RUVSeq
2.1 years ago Bogdan ▴ 670
0
votes
1
reply
856
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.5 years ago Tongjun • 0
0
votes
4
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2.9k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.5 years ago Mohamed ▴ 30
1
vote
7
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2.0k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.5 years ago by 43k • written 2.6 years ago by ▴ 50
1
vote
1
reply
936
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 20
2
votes
7
replies
2.0k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.6 years ago Jess • 0
0
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5
replies
4.7k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.0 years ago by ★ 4.6k • written 3.8 years ago by • 0
1
vote
1
reply
1.0k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.2 years ago Mallory ▴ 10
1
vote
5
replies
2.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 5 months ago by ▴ 70 • written 3.5 years ago by ▴ 50
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.6 years ago • updated 3.5 years ago reganhayward • 0
2
votes
2
replies
1.7k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.7 years ago elizabethe819 • 0
0
votes
0
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794
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.8 years ago bioinfc • 0
0
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7
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2.0k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.9 years ago by ▴ 980 • written 3.9 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 4.3 years ago by 67k • written 4.3 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 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
0
replies
788
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.6 years ago acquaviva.massimo • 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
2
votes
4
replies
2.3k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
0
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3
replies
1.2k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.9 years ago by 67k • written 4.9 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
5.1 years ago Arindam ▴ 80
0
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2
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1.9k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.2 years ago by ▴ 980 • written 5.2 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 30
0
votes
1
reply
879
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
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0
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1.0k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.6 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 5.6 years ago by ▴ 980 • written 5.7 years ago by • 0
2
votes
4
replies
2.7k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.6 years ago by ▴ 980 • written 5.7 years ago by ▴ 260
0
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0
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979
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RUVseq: Use of known controls with RUVg
RUVseq
5.7 years ago bio.erikson • 0
1
vote
3
replies
2.6k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.
Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k
You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
Votes
Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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