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goprofiles
•
reset
0
votes
1
reply
540
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db
GOfuncR
GO
GOSim
goProfiles
updated 14 months ago by
Basti
▴ 740 • written 14 months ago by
yeluo
• 0
3
votes
9
replies
2.6k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.2 years ago
artur
▴ 80
0
votes
0
replies
1.5k
views
Ontology lack in goProfiles : no BP or CC just MF
GO
goProfiles
GO
goProfiles
9.6 years ago
Arnaud Mounier
▴ 40
0
votes
0
replies
1.2k
views
error while using goProfiles package on arabidopsis entrez gene IDs
GO
Organism
goProfiles
GO
Organism
goProfiles
10.3 years ago
Marc Carlson
★ 7.2k
0
votes
0
replies
1.6k
views
error while using goProfiles package on arabidopsis entrez gene IDs
goProfiles
goProfiles
10.3 years ago
Guest User
★ 12k
0
votes
2
replies
1.0k
views
Gene Ontologies exploration
goProfiles
GeneAnswers
goProfiles
GeneAnswers
updated 10.8 years ago by
Marc Carlson
★ 7.2k • written 10.8 years ago by
Jose M Garcia Manteiga
▴ 310
0
votes
2
replies
953
views
Profiles
GO
goProfiles
GO
goProfiles
updated 11.2 years ago by
Steve Lianoglou
13k • written 11.2 years ago by
Guest User
★ 12k
0
votes
2
replies
1.3k
views
How to make my own GO.db?
GO
goProfiles
GO
goProfiles
updated 13.5 years ago by
Marc Carlson
★ 7.2k • written 13.5 years ago by
Xiaohui Wu
▴ 280
0
votes
1
reply
1.1k
views
How to cluster genes based on their GO term in Arabidopsis?
GO
Cancer
Prostate
goProfiles
GO
Cancer
Prostate
goProfiles
updated 13.5 years ago by
James W. MacDonald
64k • written 13.5 years ago by
Xiaohui Wu
▴ 280
0
votes
0
replies
707
views
Problem about using "goProfiles"
Category
goProfiles
Category
goProfiles
13.5 years ago
wei tie
▴ 30
0
votes
0
replies
968
views
How to compare GO results
Annotation
GO
topGO
goProfiles
Annotation
GO
topGO
goProfiles
14.3 years ago
Johannes Hanson
▴ 30
0
votes
0
replies
821
views
plotProfiles (goProfiles) and bitmap
GO
graph
goProfiles
GO
graph
goProfiles
14.5 years ago
Jean-Pierre Desvignes
▴ 60
0
votes
8
replies
1.6k
views
PreProcess and Limma 'done'. What directions now?
goProfiles
goProfiles
updated 14.5 years ago by
Steve Lianoglou
13k • written 14.5 years ago by
Massimo Pinto
▴ 390
0
votes
2
replies
1.0k
views
namespace error with goProfiles package
GO
mouse4302
goProfiles
GO
mouse4302
goProfiles
updated 15.5 years ago by
Alex Sanchez
▴ 20 • written 15.5 years ago by
Straubhaar, Juerg
▴ 300
14 results • Page
1 of 1
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Replies
Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
• 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R
by
Gordon Smyth
49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong
by
Gordon Smyth
49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq
by
Shaimaa Gamal
• 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change
by
James W. MacDonald
64k
You could look at my answer and extrapolate from there.
Votes
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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