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RUVSeq
•
reset
0
votes
1
reply
212
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 16 days ago by
Michael Love
42k • written 19 days ago by
Ειρήνη
• 0
0
votes
0
replies
118
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
18 days ago
Erdi
• 0
0
votes
0
replies
151
views
determine k during RUVSeq
RUVSeq
RUVnormalize
10 weeks ago
Ειρήνη
• 0
2
votes
9
replies
613
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Alexandre
• 0
3
votes
6
replies
516
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
3 months ago
nhaus
▴ 50
3
votes
2
replies
424
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
5 months ago
Shaimaa Gamal
• 0
4
votes
3
replies
508
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 5 months ago by
Gordon Smyth
51k • written 5 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
481
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 5 months ago by
James W. MacDonald
66k • written 5 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
593
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
6 months ago
ctlong
• 0
0
votes
6
replies
809
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 8 months ago by
Michael Love
42k • written 8 months ago by
myrthevanbaardwijk
• 0
5
votes
9
replies
1.6k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 3 months ago by
Gordon Smyth
51k • written 10 months ago by
Jonathan
▴ 10
3
votes
5
replies
1.1k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 10 months ago by
ATpoint
★ 4.2k • written 10 months ago by
Shashank
• 0
0
votes
4
replies
759
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
11 months ago
anne.hoffrichter
• 0
3
votes
12
replies
1.7k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 15 months ago by
Michael Love
42k • written 15 months ago by
urwah
▴ 10
1
vote
2
replies
981
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
15 months ago
AZ
▴ 30
0
votes
0
replies
448
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
15 months ago
Luca
• 0
1
vote
2
replies
1.1k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
16 months ago
garbuzov
• 0
3
votes
6
replies
1.2k
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
18 months ago • updated 16 months ago
Zainab
▴ 10
0
votes
1
reply
768
views
RUV with K more than 1.
RUVSeq
updated 18 months ago by
ATpoint
★ 4.2k • written 18 months ago by
star
▴ 10
0
votes
3
replies
1.1k
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 19 months ago by
Michael Love
42k • written 20 months ago by
Lisa
• 0
0
votes
0
replies
516
views
RUVg for SNAP-ChIP ?
RUVSeq
20 months ago
Bogdan
▴ 670
0
votes
1
reply
729
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
2.0 years ago
Tongjun
• 0
0
votes
4
replies
2.4k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
2.1 years ago
Mohamed
▴ 30
1
vote
7
replies
1.7k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq
DESeq2
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
xiaofeiwang18266
▴ 50
1
vote
1
reply
804
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 2.2 years ago by
James W. MacDonald
66k • written 2.2 years ago by
ramonfallon
▴ 20
2
votes
7
replies
1.7k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
2.2 years ago
Jess
• 0
0
votes
5
replies
4.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.5 years ago by
ATpoint
★ 4.2k • written 3.3 years ago by
Xiaojie Cheng
• 0
1
vote
1
reply
856
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2
ImpulseDE
ERCC
RUVSeq
2.8 years ago • updated 2.7 years ago
Mallory
▴ 10
1
vote
4
replies
1.7k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
3.1 years ago
xiaofeiwang18266
▴ 50
2
votes
6
replies
4.8k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
3.1 years ago
reganhayward
• 0
2
votes
2
replies
1.5k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
3.2 years ago
elizabethe819
• 0
0
votes
0
replies
699
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.3 years ago
bioinfc
• 0
0
votes
7
replies
1.7k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation
RNA-sequencing
RUVSeq
updated 3.5 years ago by
davide risso
▴ 950 • written 3.5 years ago by
Luca
• 0
5
votes
6
replies
1.7k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq
RUV
RNA-seq
updated 3.8 years ago by
James W. MacDonald
66k • written 3.8 years ago by
karissa.barthelson
▴ 20
0
votes
2
replies
1.4k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq
model.matrix
edger
updated 4.1 years ago by
James W. MacDonald
66k • written 4.1 years ago by
lucap
• 0
0
votes
7
replies
22k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
94133
• 0
0
votes
0
replies
674
views
"Frozen" RUVseq normalization
RUVseq
machine learning
4.2 years ago
acquaviva.massimo
• 0
2
votes
6
replies
1.5k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 4.2 years ago by
Gordon Smyth
51k • written 4.2 years ago by
ScA
• 0
2
votes
4
replies
1.9k
views
full confounding between batch and treatment effects
batch effects
limma
batch-correction
RNAseq
RUVseq
updated 4.2 years ago by
James W. MacDonald
66k • written 4.2 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
1.0k
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 4.5 years ago by
James W. MacDonald
66k • written 4.5 years ago by
MANYA_BIOINFO
• 0
1
vote
4
replies
2.4k
views
Removal of batch effects from RNA-seq data for WGCNA
limma
deseq2
wgcna
RUVseq
4.7 years ago
ag1805x
▴ 80
0
votes
2
replies
1.7k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.8 years ago by
davide risso
▴ 950 • written 4.8 years ago by
VeloSand
• 0
1
vote
1
reply
1.4k
views
Using RUVs with known batches
ruvseq
deseq2
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Frederik Ziebell
▴ 30
0
votes
1
reply
778
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2
ruvseq
anaquin
sequins
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
chaitra.sathyaprakash
• 0
0
votes
0
replies
909
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger
RUVseq
RUVr
GLM
RNAseq
5.1 years ago
garbuzov
• 0
0
votes
2
replies
2.6k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq
software error
edger
updated 5.1 years ago by
davide risso
▴ 950 • written 5.3 years ago by
ce.jim.san
• 0
2
votes
4
replies
2.3k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.2 years ago by
davide risso
▴ 950 • written 5.2 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
875
views
RUVseq: Use of known controls with RUVg
RUVseq
5.2 years ago
bio.erikson
• 0
1
vote
3
replies
2.3k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq
ruvseq
RUVs
DESEq2
deseq2
updated 5.4 years ago by
Gordon Smyth
51k • written 5.4 years ago by
enricoferrero
▴ 660
4
votes
4
replies
2.2k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 5.4 years ago by
Gordon Smyth
51k • written 5.4 years ago by
enricoferrero
▴ 660
50 results • Page
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Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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▴ 180
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★ 1.1k
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51k
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