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Showing :
ruvseq
•
reset
3
votes
5
replies
196
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 12 days ago by
ATpoint
★ 3.4k • written 12 days ago by
Shashank
• 0
0
votes
4
replies
262
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
7 weeks ago
anne.hoffrichter
• 0
3
votes
12
replies
779
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 5 months ago by
Michael Love
40k • written 5 months ago by
urwah
▴ 10
1
vote
2
replies
380
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
5 months ago
AZ
▴ 30
0
votes
0
replies
170
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
5 months ago
Luca
• 0
1
vote
2
replies
529
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
6 months ago
garbuzov
• 0
3
votes
6
replies
592
views
RUVr batch correction doubling number of DEGs
DESeq2
RUVSeq
7 months ago • updated 6 months ago
Zainab
• 0
0
votes
1
reply
338
views
RUV with K more than 1.
RUVSeq
updated 8 months ago by
ATpoint
★ 3.4k • written 8 months ago by
star
▴ 10
0
votes
3
replies
537
views
question about removing both known and unknown confounders
DESeq2
RUVSeq
updated 9 months ago by
Michael Love
40k • written 9 months ago by
Lisa
• 0
0
votes
0
replies
272
views
RUVg for SNAP-ChIP ?
RUVSeq
9 months ago
Bogdan
▴ 660
0
votes
1
reply
391
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
14 months ago
Tongjun
• 0
0
votes
4
replies
1.4k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
15 months ago
Mohamed
▴ 20
1
vote
7
replies
1.1k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq
DESeq2
updated 15 months ago by
Michael Love
40k • written 15 months ago by
xiaofeiwang18266
▴ 50
1
vote
1
reply
525
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 16 months ago by
James W. MacDonald
63k • written 16 months ago by
ramonfallon
• 0
2
votes
7
replies
1.1k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
16 months ago
Jess
• 0
0
votes
5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 20 months ago by
ATpoint
★ 3.4k • written 2.5 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
502
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2
ImpulseDE
ERCC
RUVSeq
23 months ago
Mallory
• 0
1
vote
4
replies
1.1k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.3 years ago
xiaofeiwang18266
▴ 50
2
votes
6
replies
3.8k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.3 years ago
reganhayward
• 0
2
votes
2
replies
1.0k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
2.4 years ago
elizabethe819
• 0
0
votes
0
replies
469
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
2.5 years ago
bioinfc
• 0
0
votes
7
replies
1.1k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation
RNA-sequencing
RUVSeq
updated 2.6 years ago by
davide risso
▴ 920 • written 2.6 years ago by
Luca
• 0
5
votes
6
replies
1.3k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq
RUV
RNA-seq
updated 3.0 years ago by
James W. MacDonald
63k • written 3.0 years ago by
karissa.barthelson
▴ 20
0
votes
2
replies
1.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq
model.matrix
edger
updated 3.3 years ago by
James W. MacDonald
63k • written 3.3 years ago by
lucap
• 0
0
votes
7
replies
19k
views
DESeq2 batch correction best practice.
deseq2
limma
RUVSeq
updated 3.3 years ago by
Michael Love
40k • written 3.3 years ago by
94133
• 0
0
votes
0
replies
424
views
"Frozen" RUVseq normalization
RUVseq
machine learning
3.3 years ago
acquaviva.massimo
• 0
2
votes
6
replies
959
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 3.4 years ago by
Gordon Smyth
48k • written 3.4 years ago by
ScA
• 0
2
votes
4
replies
1.2k
views
full confounding between batch and treatment effects
batch effects
limma
batch-correction
RNAseq
RUVseq
updated 3.4 years ago by
James W. MacDonald
63k • written 3.4 years ago by
bhakti.dwivedi
• 0
0
votes
3
replies
702
views
unable to find inherited method inRUVG
ruvseq
RUVSeq
updated 3.6 years ago by
James W. MacDonald
63k • written 3.6 years ago by
MANYA_BIOINFO
• 0
1
vote
4
replies
1.8k
views
Removal of batch effects from RNA-seq data for WGCNA
limma
deseq2
wgcna
RUVseq
3.9 years ago
ag1805x
▴ 80
0
votes
2
replies
1.2k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.0 years ago by
davide risso
▴ 920 • written 4.0 years ago by
VeloSand
• 0
1
vote
1
reply
1.0k
views
Using RUVs with known batches
ruvseq
deseq2
updated 4.1 years ago by
Michael Love
40k • written 4.1 years ago by
Frederik Ziebell
▴ 10
0
votes
1
reply
543
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2
ruvseq
anaquin
sequins
updated 4.3 years ago by
Michael Love
40k • written 4.3 years ago by
chaitra.sathyaprakash
• 0
0
votes
0
replies
652
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger
RUVseq
RUVr
GLM
RNAseq
4.3 years ago
garbuzov
• 0
0
votes
2
replies
2.2k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq
software error
edger
updated 4.3 years ago by
davide risso
▴ 920 • written 4.4 years ago by
ce.jim.san
• 0
2
votes
4
replies
1.7k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 4.4 years ago by
davide risso
▴ 920 • written 4.4 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
599
views
RUVseq: Use of known controls with RUVg
RUVseq
4.4 years ago
bio.erikson
• 0
1
vote
3
replies
1.7k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq
ruvseq
RUVs
DESEq2
deseq2
updated 4.6 years ago by
Gordon Smyth
48k • written 4.6 years ago by
enricoferrero
▴ 660
4
votes
4
replies
1.5k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 4.6 years ago by
Gordon Smyth
48k • written 4.6 years ago by
enricoferrero
▴ 660
0
votes
1
reply
881
views
merging RUV-corrected datasets in DESEq
deseq2
glm
zinbwave
ruvseq
updated 4.8 years ago by
Michael Love
40k • written 4.8 years ago by
Jakub
▴ 50
0
votes
0
replies
982
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
4.8 years ago
kbobowik
• 0
0
votes
8
replies
1.7k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 4.9 years ago by
davide risso
▴ 920 • written 4.9 years ago by
capricygcapricyg
• 0
0
votes
2
replies
1.6k
views
determine k during RUVSeq
ruvseq
updated 4.9 years ago by
davide risso
▴ 920 • written 4.9 years ago by
capricygcapricyg
• 0
1
vote
9
replies
2.1k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 5.0 years ago by
davide risso
▴ 920 • written 5.0 years ago by
zoppoli pietro
▴ 10
2
votes
3
replies
1.0k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger
design matrix
paired samples
ruvseq
updated 5.1 years ago by
James W. MacDonald
63k • written 5.1 years ago by
ChrisM
• 0
1
vote
3
replies
1.2k
views
Global expression shift using RUVSeq
ruvseq
rnaseq
normalization
differential expression
updated 5.2 years ago by
davide risso
▴ 920 • written 5.2 years ago by
Leon
• 0
2
votes
2
replies
1.7k
views
RUVg with differential transcript expression?
ruvseq
sleuth
updated 5.7 years ago by
davide risso
▴ 920 • written 5.7 years ago by
Brian Gudenas
• 0
6
votes
2
replies
2.7k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2
ruvseq
spike-in
time course
time series
updated 5.8 years ago by
davide risso
▴ 920 • written 5.8 years ago by
staceyborrego
▴ 20
0
votes
3
replies
1.6k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2
ruvseq
rna-seq
batch effect
updated 5.8 years ago by
Michael Love
40k • written 5.8 years ago by
dbouzo
• 0
1
vote
1
reply
1.3k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 5.9 years ago by
davide risso
▴ 920 • written 5.9 years ago by
llo
▴ 10
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Comment: DataFrame Construction With Non-standard Column
by
ATpoint
★ 3.4k
Out of interest, `SimpleList()` works without `I()`, why is that?
Answer: DataFrame Construction With Non-standard Column
by
Hervé Pagès
16k
You need to protect the list by wrapping it in `I()`, otherwise the `DataFrame()` constructor interprets it as a list of 3 columns (so it t…
Comment: Speeding up of DelayedArray::write_block()
by
Koki
▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block()
by
Koki
▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block
by
Hervé Pagès
16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Votes
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
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