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Showing :
ruvseq
•
reset
2
votes
2
replies
469
views
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
449
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 4 months ago by
Michael Love
42k • written 4 months ago by
Ειρήνη
• 0
1
vote
0
replies
275
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
4 months ago
Erdi
▴ 10
0
votes
0
replies
260
views
determine k during RUVSeq
RUVSeq
RUVnormalize
6 months ago
Ειρήνη
• 0
2
votes
9
replies
939
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 months ago by
James W. MacDonald
67k • written 7 months ago by
Alexandre
• 0
3
votes
6
replies
827
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
7 months ago
nhaus
▴ 70
3
votes
2
replies
566
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
9 months ago
Shaimaa Gamal
• 0
4
votes
3
replies
688
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 9 months ago by
Gordon Smyth
51k • written 9 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
660
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 9 months ago by
James W. MacDonald
67k • written 9 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
783
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
10 months ago
ctlong
• 0
0
votes
6
replies
966
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 12 months ago by
Michael Love
42k • written 12 months ago by
myrthevanbaardwijk
• 0
5
votes
9
replies
1.9k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 7 months ago by
Gordon Smyth
51k • written 14 months ago by
Jonathan
▴ 10
3
votes
5
replies
1.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 14 months ago by
ATpoint
★ 4.5k • written 14 months ago by
Shashank
• 0
0
votes
4
replies
951
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
Michael Love
42k • written 19 months ago by
urwah
▴ 10
1
vote
2
replies
1.1k
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
19 months ago
AZ
▴ 30
0
votes
0
replies
541
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
19 months ago
Luca
• 0
1
vote
2
replies
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
22 months ago • updated 20 months ago
Zainab
▴ 20
0
votes
1
reply
918
views
RUV with K more than 1.
RUVSeq
updated 22 months ago by
ATpoint
★ 4.5k • written 22 months ago by
star
▴ 10
0
votes
3
replies
1.2k
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 23 months ago by
Michael Love
42k • written 23 months ago by
Lisa
• 0
0
votes
0
replies
631
views
RUVg for SNAP-ChIP ?
RUVSeq
23 months ago
Bogdan
▴ 670
0
votes
1
reply
832
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
2.4 years ago
Tongjun
• 0
0
votes
4
replies
2.8k
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
2.0k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq
DESeq2
updated 2.4 years ago by
Michael Love
42k • written 2.5 years ago by
xiaofeiwang18266
▴ 50
1
vote
1
reply
907
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 2.5 years ago by
James W. MacDonald
67k • written 2.5 years ago by
ramonfallon
▴ 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 2.9 years ago by
ATpoint
★ 4.5k • written 3.7 years ago by
Xiaojie Cheng
• 0
1
vote
1
reply
981
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
replies
2.0k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
updated 3 months ago by
BioinfGuru
▴ 70 • written 3.4 years ago by
xiaofeiwang18266
▴ 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()
3.6 years ago
elizabethe819
• 0
0
votes
0
replies
770
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
votes
7
replies
1.9k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation
RNA-sequencing
RUVSeq
updated 3.8 years ago by
davide risso
▴ 980 • written 3.8 years ago by
Luca
• 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
James W. MacDonald
67k • written 4.2 years ago by
karissa.barthelson
▴ 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
James W. MacDonald
67k • written 4.4 years ago by
lucap
• 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
94133
• 0
0
votes
0
replies
763
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
Gordon Smyth
51k • written 4.5 years ago by
ScA
• 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
James W. MacDonald
67k • written 4.5 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
1.1k
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
MANYA_BIOINFO
• 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
1.9k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.1 years ago by
davide risso
▴ 980 • written 5.1 years ago by
VeloSand
• 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq
deseq2
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
Frederik Ziebell
▴ 30
0
votes
1
reply
856
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2
ruvseq
anaquin
sequins
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
chaitra.sathyaprakash
• 0
0
votes
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
davide risso
▴ 980 • written 5.6 years ago by
ce.jim.san
• 0
2
votes
4
replies
2.6k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.5 years ago by
davide risso
▴ 980 • written 5.5 years ago by
Jon Bråte
▴ 260
0
votes
0
replies
952
views
RUVseq: Use of known controls with RUVg
RUVseq
5.6 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 5.8 years ago by
Gordon Smyth
51k • written 5.8 years ago by
enricoferrero
▴ 660
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Comment: Differene between the Wald and LRT test for time-series gene expression data
by
Denise
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This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units
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The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
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