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ruv
•
reset
1
vote
2
replies
1.4k
views
RUV4 for microarrays
RUV4
RUV
Microarray
3.1 years ago
Antonio
• 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 3.7 years ago by
James W. MacDonald
66k • written 3.7 years ago by
karissa.barthelson
▴ 20
0
votes
1
reply
1.7k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 4.1 years ago by
hermidalc
▴ 20 • written 4.9 years ago by
raf4
▴ 20
0
votes
3
replies
992
views
Highly variable gene analysis including RUVs batch correction
deseq2
RUV
batch
highly variable genes
updated 4.3 years ago by
tmms
• 0 • written 4.3 years ago by
f_pardow
• 0
0
votes
1
reply
1.2k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2
ruv
batch
updated 4.7 years ago by
Michael Love
42k • written 4.7 years ago by
r.tom
• 0
0
votes
0
replies
938
views
missMethyl EPIC manifest update
missmethyl
epic
illuminahumanmethylationepicanno.ilm10b4.hg19.
ruv
5.8 years ago
peter.fransquet
• 0
0
votes
0
replies
918
views
which value from ruvadj in missMethyl can present methylation status
methylation
missmethyl
RUV
batch effect
6.1 years ago
RC
• 0
0
votes
0
replies
936
views
MissMethyl: Sample size and control probes
missmethyl
RUV
control probes
6.1 years ago
Taub, Margaret
▴ 10
2
votes
9
replies
2.6k
views
Zero inflation in RUV normalization and DE for single cell data
ruv
ruvseq
ruvnormalize
single-cell
zero-inflated
updated 6.9 years ago by
davide risso
▴ 950 • written 6.9 years ago by
Nik Tuzov
▴ 80
1
vote
3
replies
2.3k
views
Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV
ruvseq
ruvr
ruvnormalize
single cell
6.9 years ago
Nik Tuzov
▴ 80
0
votes
0
replies
932
views
Differential expressed genes between different samples in RUVseq
rnaseq
ruv
differential gene expression
R
7.0 years ago
manish20072013
• 0
3
votes
4
replies
3.2k
views
Single cells batch effects
RUV
single cell
batch effect
7.2 years ago
ribioinfo
▴ 100
0
votes
0
replies
1.0k
views
Has anyone used the RUV package for Microbiome data?
ruv
7.3 years ago
sasha
• 0
0
votes
1
reply
2.3k
views
Can FPKM or TPM values be used as RUVs input ?
ruvseq
ruvg
ruv
updated 7.4 years ago by
davide risso
▴ 950 • written 7.5 years ago by
weiwsmiling
• 0
0
votes
0
replies
1.1k
views
Bach effect and PEER/RUV correction on large population
methylation
gene expression
sva
batch effect
ruv
7.5 years ago
carleshf
▴ 10
2
votes
1
reply
1.6k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq
RUV
ruvnormalize
ruvg
7.9 years ago
anthonycolombo60
• 0
0
votes
5
replies
2.3k
views
RUVseq for microRNAs
ruvseq
ruv
microrna
8.9 years ago
sergio.espeso-gil
• 0
0
votes
1
reply
1.6k
views
normalised data after RUV2( )
ruv
microarray
updated 8.9 years ago by
gthm
▴ 30 • written 9.1 years ago by
Pauly Lin
▴ 150
3
votes
2
replies
2.7k
views
Normalisation before RUVg and RUV2?
ruvseq
ruv
updated 9.1 years ago by
davide risso
▴ 950 • written 9.1 years ago by
Pauly Lin
▴ 150
1
vote
9
replies
2.7k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
9.1 years ago
sergio.espeso-gil
• 0
20 results • Page
1 of 1
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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