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ruvseq
•
reset
0
votes
0
replies
65
views
determine k during RUVSeq
RUVSeq
RUVnormalize
6 days ago
Ειρήνη
• 0
2
votes
9
replies
432
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 26 days ago by
James W. MacDonald
66k • written 27 days ago by
Alexandre
• 0
3
votes
6
replies
317
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
3
votes
2
replies
324
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
3 months ago
Shaimaa Gamal
• 0
4
votes
3
replies
389
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
396
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
491
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago
ctlong
• 0
0
votes
6
replies
714
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 6 months ago by
Michael Love
42k • written 6 months ago by
myrthevanbaardwijk
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
5
replies
902
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Shashank
• 0
0
votes
4
replies
661
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
9 months ago
anne.hoffrichter
• 0
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 13 months ago by
Michael Love
42k • written 13 months ago by
urwah
▴ 10
1
vote
2
replies
884
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
13 months ago
AZ
▴ 30
0
votes
0
replies
401
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
13 months ago
Luca
• 0
1
vote
2
replies
1.0k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
14 months ago
garbuzov
• 0
3
votes
6
replies
1.1k
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
15 months ago • updated 14 months ago
Zainab
▴ 10
0
votes
1
reply
667
views
RUV with K more than 1.
RUVSeq
updated 16 months ago by
ATpoint
★ 4.1k • written 16 months ago by
star
▴ 10
0
votes
3
replies
1.0k
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 17 months ago by
Michael Love
42k • written 17 months ago by
Lisa
• 0
0
votes
0
replies
473
views
RUVg for SNAP-ChIP ?
RUVSeq
17 months ago
Bogdan
▴ 670
0
votes
1
reply
665
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
22 months ago
Tongjun
• 0
0
votes
4
replies
2.2k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
23 months ago
Mohamed
▴ 30
1
vote
7
replies
1.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq
DESeq2
updated 23 months ago by
Michael Love
42k • written 23 months ago by
xiaofeiwang18266
▴ 50
1
vote
1
reply
754
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 24 months ago by
James W. MacDonald
66k • written 24 months ago by
ramonfallon
▴ 20
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
2.0 years ago • updated 24 months ago
Jess
• 0
0
votes
5
replies
3.7k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.4 years ago by
ATpoint
★ 4.1k • written 3.2 years ago by
Xiaojie Cheng
• 0
1
vote
1
reply
783
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2
ImpulseDE
ERCC
RUVSeq
2.6 years ago • updated 2.5 years ago
Mallory
▴ 10
1
vote
4
replies
1.6k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.9 years ago
xiaofeiwang18266
▴ 50
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.9 years ago
reganhayward
• 0
2
votes
2
replies
1.4k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
3.1 years ago
elizabethe819
• 0
0
votes
0
replies
648
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.2 years ago
bioinfc
• 0
0
votes
7
replies
1.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation
RNA-sequencing
RUVSeq
updated 3.3 years ago by
davide risso
▴ 950 • written 3.3 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 3.7 years ago by
James W. MacDonald
66k • written 3.7 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 3.9 years ago by
James W. MacDonald
66k • written 3.9 years ago by
lucap
• 0
0
votes
7
replies
21k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
94133
• 0
0
votes
0
replies
617
views
"Frozen" RUVseq normalization
RUVseq
machine learning
4.0 years ago
acquaviva.massimo
• 0
2
votes
6
replies
1.4k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
ScA
• 0
2
votes
4
replies
1.7k
views
full confounding between batch and treatment effects
batch effects
limma
batch-correction
RNAseq
RUVseq
updated 4.0 years ago by
James W. MacDonald
66k • written 4.0 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
991
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 4.3 years ago by
James W. MacDonald
66k • written 4.3 years ago by
MANYA_BIOINFO
• 0
1
vote
4
replies
2.3k
views
Removal of batch effects from RNA-seq data for WGCNA
limma
deseq2
wgcna
RUVseq
4.5 years ago
ag1805x
▴ 80
0
votes
2
replies
1.6k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.6 years ago by
davide risso
▴ 950 • written 4.6 years ago by
VeloSand
• 0
1
vote
1
reply
1.3k
views
Using RUVs with known batches
ruvseq
deseq2
updated 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
Frederik Ziebell
▴ 20
0
votes
1
reply
737
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2
ruvseq
anaquin
sequins
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
chaitra.sathyaprakash
• 0
0
votes
0
replies
855
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 5.0 years ago by
davide risso
▴ 950 • written 5.1 years ago by
ce.jim.san
• 0
2
votes
4
replies
2.2k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.0 years ago by
davide risso
▴ 950 • written 5.0 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
831
views
RUVseq: Use of known controls with RUVg
RUVseq
5.1 years ago
bio.erikson
• 0
1
vote
3
replies
2.2k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq
ruvseq
RUVs
DESEq2
deseq2
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
enricoferrero
▴ 660
4
votes
4
replies
2.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
Jakub
▴ 50
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
5.5 years ago
kbobowik
• 0
50 results • Page
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Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Happiness
• 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
mohammedtoufiq91
▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: recount3 problem downloading data from source sra
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