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RUVNormalize
•
reset
1
vote
2
replies
818
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
12 months ago
AZ
▴ 30
0
votes
4
replies
2.1k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
22 months ago
Mohamed
▴ 30
0
votes
1
reply
608
views
Is RUVnormalize applicable to small dataset?
RUVnormalize
protein mi
5.5 years ago
losik
• 0
0
votes
2
replies
991
views
RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
RUVnormalize
limma
corrected expression matrix
microarray
updated 6.3 years ago by
Dario Strbenac
★ 1.5k • written 6.3 years ago by
massimo.acquaviva.78
• 0
2
votes
9
replies
2.5k
views
Zero inflation in RUV normalization and DE for single cell data
ruv
ruvseq
ruvnormalize
single-cell
zero-inflated
updated 6.7 years ago by
davide risso
▴ 950 • written 6.7 years ago by
Nik Tuzov
▴ 80
1
vote
3
replies
2.2k
views
Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV
ruvseq
ruvr
ruvnormalize
single cell
6.7 years ago
Nik Tuzov
▴ 80
2
votes
1
reply
1.3k
views
Decide normalisation method in RUVseq for RNAseq data
edger
ruvseq
rnaseq
normalization
ruvnormalize
updated 6.8 years ago by
davide risso
▴ 950 • written 6.8 years ago by
manish20072013
• 0
2
votes
1
reply
1.5k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq
RUV
ruvnormalize
ruvg
7.8 years ago
anthonycolombo60
• 0
2
votes
6
replies
1.4k
views
effect of polyploidy level on RUVs normalisation
normalization
ruvseq
ruvnormalize
ruvs eda
8.0 years ago
thomas.wolfe
• 0
0
votes
0
replies
1.3k
views
Technical Replicates and RUVs Normalisation
rnaseq
ruvnormalize
normalization
technical replicates
8.4 years ago
thomas.wolfe
• 0
1
vote
1
reply
1.3k
views
RUVnormalize- should input be pre-normalized?
ruvnormalize
microarray
normalization
updated 8.8 years ago by
laurent.jacob
▴ 10 • written 8.9 years ago by
Cornwell, Adam
▴ 110
2
votes
1
reply
1.2k
views
naiveRandRUV Error When k is 1
RUVNormalize
Subsetting
updated 8.8 years ago by
laurent.jacob
▴ 10 • written 8.9 years ago by
Dario Strbenac
★ 1.5k
12 results • Page
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Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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