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reset
1
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4
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23k
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edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
11.0 years ago
ccheung
• 0
3
votes
7
replies
7.8k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 9.5 years ago by
Gordon Smyth
53k • written 9.6 years ago by
mnaymik
▴ 10
3
votes
3
replies
4.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 4.4 years ago by
IIart.hubII
• 0 • written 8.2 years ago by
svlachavas
▴ 840
2
votes
4
replies
4.3k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
alakatos
▴ 130
0
votes
2
replies
3.9k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
fawazfebin
▴ 60
3
votes
6
replies
3.4k
views
How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
edger
raw reads
TMM normalised values
DGEList
differential gene expression
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
benedict.ng
▴ 20
1
vote
4
replies
3.1k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.8 years ago
aljoscha.leusmann
• 0
0
votes
1
reply
2.8k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
belmore
• 0
0
votes
2
replies
2.5k
views
create DGElist Object
edger
DGElist
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
naser.sadri
• 0
0
votes
4
replies
2.3k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 7.5 years ago by
Gordon Smyth
53k • written 7.5 years ago by
Kevin
• 0
1
vote
1
reply
1.5k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 4.7 years ago by
Gordon Smyth
53k • written 4.7 years ago by
Alex
• 0
0
votes
0
replies
1.4k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
7.9 years ago
Larry K.
• 0
2
votes
2
replies
1.1k
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
Fiona
• 0
0
votes
2
replies
764
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
21 months ago
prity6459
• 0
14 results • Page
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Comment: DiffBind plot.profile error
by
a2sahaaaq2c
• 0
To resolve technical errors like installation failures or login issues, first ensure your device allows in the security settings and that…
Comment: soGGi error
by
shepherl
4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
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