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edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.2 years ago
ccheung
• 0
3
votes
7
replies
6.6k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
mnaymik
▴ 10
3
votes
3
replies
3.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 2.6 years ago by
IIart.hubII
• 0 • written 6.4 years ago by
svlachavas
▴ 830
2
votes
4
replies
3.1k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
alakatos
▴ 130
0
votes
2
replies
3.0k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
fawazfebin
▴ 60
3
votes
6
replies
2.4k
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 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
benedict.ng
▴ 20
0
votes
1
reply
2.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
belmore
• 0
1
vote
4
replies
2.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.0 years ago
aljoscha.leusmann
• 0
0
votes
4
replies
1.7k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
Kevin
• 0
0
votes
2
replies
1.7k
views
create DGElist Object
edger
DGElist
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
naser.sadri
• 0
0
votes
0
replies
910
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.1 years ago
Larry K.
• 0
1
vote
1
reply
824
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Alex
• 0
2
votes
2
replies
597
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Fiona
• 0
13 results • Page
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Answer: OrgDb for maize
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I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
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Thanks Peter!
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Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
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They are reorder in the decreasing order.
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Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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