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ruvseq
•
reset
0
votes
0
replies
42
views
determine k during RUVSeq
RUVSeq
RUVnormalize
1 day ago
Ειρήνη
• 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Alexandre
• 0
3
votes
6
replies
305
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
3
votes
2
replies
317
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
3 months ago
Shaimaa Gamal
• 0
4
votes
3
replies
378
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
386
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
483
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago
ctlong
• 0
0
votes
6
replies
696
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 5 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
891
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
649
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
872
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
13 months ago
AZ
▴ 30
0
votes
0
replies
400
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
661
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
0
replies
470
views
RUVg for SNAP-ChIP ?
RUVSeq
17 months ago
Bogdan
▴ 670
0
votes
3
replies
1000
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
1
reply
656
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
752
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 24 months ago by
James W. MacDonald
65k • written 24 months ago by
ramonfallon
▴ 20
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
24 months ago
Jess
• 0
1
vote
1
reply
779
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()
3.0 years ago
elizabethe819
• 0
0
votes
0
replies
646
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
5
replies
3.6k
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
★ 4.1k • written 3.2 years ago by
Xiaojie Cheng
• 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
65k • 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
65k • 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
609
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
65k • written 4.0 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
986
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 4.3 years ago by
James W. MacDonald
65k • 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
733
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
850
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
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
827
views
RUVseq: Use of known controls with RUVg
RUVseq
5.0 years ago
bio.erikson
• 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 5.1 years ago by
ce.jim.san
• 0
4
votes
4
replies
2.1k
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
1
vote
3
replies
2.2k
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 5.3 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: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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