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ruv
•
reset
0
votes
1
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403
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 3 months ago by
Michael Love
42k • written 3 months ago by
Ειρήνη
• 0
1
vote
2
replies
1.6k
views
RUV4 for microarrays
RUV4
RUV
Microarray
3.5 years ago
Antonio
• 0
5
votes
6
replies
1.8k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq
RUV
RNA-seq
updated 4.1 years ago by
James W. MacDonald
67k • written 4.1 years ago by
karissa.barthelson
▴ 20
0
votes
1
reply
1.8k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 4.5 years ago by
hermidalc
▴ 20 • written 5.2 years ago by
raf4
▴ 30
0
votes
3
replies
1.2k
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.7 years ago by
tmms
• 0 • written 4.7 years ago by
f_pardow
• 0
0
votes
1
reply
1.4k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
r.tom
• 0
0
votes
0
replies
1.0k
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
6.2 years ago
peter.fransquet
• 0
0
votes
0
replies
1.0k
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
6.5 years ago
RC
• 0
0
votes
0
replies
1.1k
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
6.5 years ago
Taub, Margaret
▴ 10
2
votes
9
replies
2.9k
views
Zero inflation in RUV normalization and DE for single cell data
ruv
ruvseq
ruvnormalize
single-cell
zero-inflated
updated 7.2 years ago by
davide risso
▴ 980 • written 7.2 years ago by
Nik Tuzov
▴ 90
1
vote
3
replies
2.6k
views
Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV
ruvseq
ruvr
ruvnormalize
single cell
7.2 years ago
Nik Tuzov
▴ 90
0
votes
0
replies
1.0k
views
Differential expressed genes between different samples in RUVseq
rnaseq
ruv
differential gene expression
R
7.3 years ago
manish20072013
• 0
3
votes
4
replies
3.4k
views
Single cells batch effects
RUV
single cell
batch effect
7.6 years ago
ribioinfo
▴ 100
0
votes
0
replies
1.1k
views
Has anyone used the RUV package for Microbiome data?
ruv
7.7 years ago
sasha
• 0
0
votes
1
reply
2.5k
views
Can FPKM or TPM values be used as RUVs input ?
ruvseq
ruvg
ruv
updated 7.7 years ago by
davide risso
▴ 980 • written 7.8 years ago by
weiwsmiling
• 0
0
votes
0
replies
1.2k
views
Bach effect and PEER/RUV correction on large population
methylation
gene expression
sva
batch effect
ruv
7.9 years ago • updated 7.8 years ago
carleshf
▴ 10
2
votes
1
reply
1.7k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq
RUV
ruvnormalize
ruvg
8.3 years ago
anthonycolombo60
• 0
0
votes
5
replies
2.5k
views
RUVseq for microRNAs
ruvseq
ruv
microrna
9.3 years ago • updated 9.2 years ago
sergio.espeso-gil
• 0
0
votes
1
reply
1.7k
views
normalised data after RUV2( )
ruv
microarray
updated 9.3 years ago by
gthm
▴ 30 • written 9.4 years ago by
Pauly Lin
▴ 160
3
votes
2
replies
2.8k
views
Normalisation before RUVg and RUV2?
ruvseq
ruv
updated 9.5 years ago by
davide risso
▴ 980 • written 9.5 years ago by
Pauly Lin
▴ 160
1
vote
9
replies
2.9k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
9.5 years ago
sergio.espeso-gil
• 0
21 results • Page
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Recent ...
Replies
Answer: Analysis of 2*4 factorial design
by
Gordon Smyth
51k
This is covered by Section 9.5 of the limma User's Guide. The analysis with a single-factor is much better. Your definition of A2 vs A1 …
Comment: Zero intra-block correlation in RRBS analysis using voomLmFit with block
by
Gordon Smyth
51k
It might be ok to estimate the intrablock correlation from the M-values. But then, if you do that, you may as well do the whole analysis in…
Answer: limma technical repeat correction
by
Gordon Smyth
51k
The technical samples should be averaged. Then use duplicateCorrelation() with block=PatientID.
Comment: New to mass spec data analysis
by
abhisek001
• 0
Thanks for your kind responses.
Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP
by
Anni
• 0
I encountered the same problem. Problem seems to be "make_se()" function that does *not* use variable 'label' to bind colData to assay, but…
Votes
Differential expression analysis starting from TPM data
Answer: How to identify top most variable genes from log2 normalized data?
Answer: How to identify top most variable genes from log2 normalized data?
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Answer: clusterProfiler enrichGO on only T-cell related GO terms
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