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DGEList
•
reset
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
27 days ago
prity6459
• 0
2
votes
2
replies
630
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Fiona
• 0
1
vote
1
reply
851
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Alex
• 0
0
votes
2
replies
1.7k
views
create DGElist Object
edger
DGElist
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
naser.sadri
• 0
0
votes
4
replies
1.7k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
Kevin
• 0
1
vote
4
replies
2.1k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.1 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
931
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.2 years ago
Larry K.
• 0
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
3
votes
3
replies
3.7k
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 6.5 years ago by
svlachavas
▴ 830
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
2
votes
4
replies
3.2k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 6.9 years ago by
Gordon Smyth
50k • written 6.9 years ago by
alakatos
▴ 130
3
votes
6
replies
2.5k
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 7.8 years ago by
Steve Lianoglou
★ 13k • written 7.8 years ago by
benedict.ng
▴ 20
3
votes
7
replies
6.7k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
mnaymik
▴ 10
1
vote
4
replies
20k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.3 years ago
ccheung
• 0
14 results • Page
1 of 1
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Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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