Showing : RUVseq • reset
2
votes
2
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482
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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
461
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 4 months ago by 43k • written 4 months ago by • 0
1
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0
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284
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
4 months ago Erdi ▴ 10
0
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0
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268
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determine k during RUVSeq
RUVSeq RUVnormalize
6 months ago Ειρήνη • 0
2
votes
9
replies
966
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 months ago by 67k • written 7 months ago by • 0
3
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6
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850
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
7 months ago nhaus ▴ 70
3
votes
2
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578
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
9 months ago Shaimaa Gamal • 0
4
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3
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705
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
2
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3
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671
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 months ago by 67k • written 10 months ago by • 0
2
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5
replies
794
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
10 months ago ctlong • 0
0
votes
6
replies
979
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 12 months ago by 43k • written 13 months ago by • 0
5
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9
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2.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 7 months ago by 52k • written 14 months ago by ▴ 10
3
votes
5
replies
1.5k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 14 months ago by ★ 4.6k • written 14 months ago by • 0
0
votes
4
replies
958
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
16 months ago anne.hoffrichter • 0
3
votes
12
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2.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 19 months ago by 43k • written 19 months ago by ▴ 10
1
vote
2
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1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
20 months ago • updated 19 months ago AZ ▴ 30
0
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0
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547
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
20 months ago Luca • 0
1
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2
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1.4k
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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
22 months ago • updated 20 months ago Zainab ▴ 20
0
votes
1
reply
931
views
RUV with K more than 1.
RUVSeq
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 10
0
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3
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1.2k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 23 months ago by 43k • written 2.0 years ago by • 0
0
votes
0
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634
views
RUVg for SNAP-ChIP ?
RUVSeq
2.0 years ago Bogdan ▴ 670
0
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1
reply
838
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.4 years ago Tongjun • 0
0
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4
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2.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.5 years ago • updated 2.4 years ago Mohamed ▴ 30
1
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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 2.5 years ago by ▴ 50
1
vote
1
reply
913
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
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5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
1
vote
1
reply
988
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.1 years ago Mallory ▴ 10
1
vote
5
replies
2.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 4 months ago by ▴ 70 • written 3.5 years ago by ▴ 50
2
votes
6
replies
5.3k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
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()
3.6 years ago elizabethe819 • 0
0
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0
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779
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.7 years ago bioinfc • 0
0
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7
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1.9k
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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
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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 43k • written 4.4 years ago by • 0
0
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0
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770
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 4.6 years ago by 52k • written 4.6 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 4.6 years ago by 67k • written 4.6 years ago by • 0
0
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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
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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
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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
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1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
0
votes
1
reply
859
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.5 years ago by 43k • written 5.5 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
5.5 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 5.6 years ago by ▴ 980 • written 5.6 years ago by ▴ 260
0
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0
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957
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RUVseq: Use of known controls with RUVg
RUVseq
5.6 years ago bio.erikson • 0
1
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3
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2.5k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 660
50 results • Page 1 of 1
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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