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Showing :
RUVseq
•
reset
3
votes
6
replies
201
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
7 days ago
nhaus
▴ 30
3
votes
2
replies
258
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
10 weeks ago
Shaimaa Gamal
• 0
4
votes
3
replies
313
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
329
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Shaimaa Gamal
• 0
2
votes
5
replies
424
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
3 months ago
ctlong
• 0
0
votes
6
replies
653
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 4 months ago by
Michael Love
41k • written 5 months ago by
myrthevanbaardwijk
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 15 hours ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
3
votes
5
replies
794
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Shashank
• 0
0
votes
4
replies
606
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
8 months ago
anne.hoffrichter
• 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 12 months ago by
Michael Love
41k • written 12 months ago by
urwah
▴ 10
1
vote
2
replies
817
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
12 months ago
AZ
▴ 30
0
votes
0
replies
372
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
12 months ago
Luca
• 0
1
vote
2
replies
979
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
13 months ago
garbuzov
• 0
3
votes
6
replies
1.0k
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
14 months ago • updated 13 months ago
Zainab
• 0
0
votes
1
reply
629
views
RUV with K more than 1.
RUVSeq
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
star
▴ 10
0
votes
3
replies
966
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 16 months ago by
Michael Love
41k • written 16 months ago by
Lisa
• 0
0
votes
0
replies
450
views
RUVg for SNAP-ChIP ?
RUVSeq
16 months ago
Bogdan
▴ 670
0
votes
1
reply
606
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
21 months ago
Tongjun
• 0
0
votes
4
replies
2.1k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
22 months ago
Mohamed
▴ 30
1
vote
7
replies
1.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq
DESeq2
updated 22 months ago by
Michael Love
41k • written 22 months ago by
xiaofeiwang18266
▴ 50
1
vote
1
reply
732
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
ramonfallon
▴ 20
2
votes
7
replies
1.5k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
23 months ago
Jess
• 0
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.3 years ago by
ATpoint
★ 4.0k • written 3.1 years ago by
Xiaojie Cheng
• 0
1
vote
1
reply
744
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2
ImpulseDE
ERCC
RUVSeq
2.5 years ago
Mallory
▴ 10
1
vote
4
replies
1.5k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.8 years ago
xiaofeiwang18266
▴ 50
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.8 years ago
reganhayward
• 0
2
votes
2
replies
1.3k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
3.0 years ago
elizabethe819
• 0
0
votes
0
replies
627
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.1 years ago
bioinfc
• 0
0
votes
7
replies
1.5k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation
RNA-sequencing
RUVSeq
updated 3.2 years ago by
davide risso
▴ 950 • written 3.2 years ago by
Luca
• 0
5
votes
6
replies
1.6k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq
RUV
RNA-seq
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
karissa.barthelson
▴ 20
0
votes
2
replies
1.3k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq
model.matrix
edger
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
lucap
• 0
0
votes
7
replies
21k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
94133
• 0
0
votes
0
replies
574
views
"Frozen" RUVseq normalization
RUVseq
machine learning
3.9 years ago
acquaviva.massimo
• 0
2
votes
6
replies
1.3k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
ScA
• 0
2
votes
4
replies
1.6k
views
full confounding between batch and treatment effects
batch effects
limma
batch-correction
RNAseq
RUVseq
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
957
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
MANYA_BIOINFO
• 0
1
vote
4
replies
2.2k
views
Removal of batch effects from RNA-seq data for WGCNA
limma
deseq2
wgcna
RUVseq
4.4 years ago
ag1805x
▴ 80
0
votes
2
replies
1.5k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.5 years ago by
davide risso
▴ 950 • written 4.5 years ago by
VeloSand
• 0
1
vote
1
reply
1.3k
views
Using RUVs with known batches
ruvseq
deseq2
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
Frederik Ziebell
▴ 20
0
votes
1
reply
709
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2
ruvseq
anaquin
sequins
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
chaitra.sathyaprakash
• 0
0
votes
0
replies
827
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger
RUVseq
RUVr
GLM
RNAseq
4.9 years ago
garbuzov
• 0
0
votes
2
replies
2.5k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq
software error
edger
updated 4.9 years ago by
davide risso
▴ 950 • written 5.0 years ago by
ce.jim.san
• 0
2
votes
4
replies
2.1k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 4.9 years ago by
davide risso
▴ 950 • written 4.9 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
798
views
RUVseq: Use of known controls with RUVg
RUVseq
5.0 years ago
bio.erikson
• 0
1
vote
3
replies
2.1k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq
ruvseq
RUVs
DESEq2
deseq2
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
enricoferrero
▴ 660
4
votes
4
replies
2.0k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
Jakub
▴ 50
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
5.4 years ago
kbobowik
• 0
0
votes
8
replies
2.2k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 5.4 years ago by
davide risso
▴ 950 • written 5.4 years ago by
capricygcapricyg
▴ 10
0
votes
2
replies
2.0k
views
determine k during RUVSeq
ruvseq
updated 5.5 years ago by
davide risso
▴ 950 • written 5.5 years ago by
capricygcapricyg
▴ 10
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Comment: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded
by
W. Evan Johnson
▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis
by
Alejandro Reyes
★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object
by
Alejandro Reyes
★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Answer: rlog transformation
by
Michael Love
41k
It is dependent on the other samples in the dataset.
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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