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GO
•
reset
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 years ago by
nw328
▴ 20
0
votes
3
replies
9.7k
views
FW: uninstalling
GO
GO
updated 19.4 years ago by
Jeff Gentry
★ 3.9k • written 19.4 years ago by
Law, Annie
▴ 70
0
votes
2
replies
9.2k
views
an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
GO
hgug4112a
GO
hgug4112a
updated 14.6 years ago by
James W. MacDonald
65k • written 14.5 years ago by
Massimo Pinto
▴ 390
0
votes
2
replies
8.9k
views
Clusterprofiler error: No gene can be mapped
software error
go
annotation
clusterProfiler
updated 12 months ago by
tarltonuk2089
• 0 • written 4.1 years ago by
tianshenbio
• 0
3
votes
3
replies
8.7k
views
error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()
annotationforge
Annotation
GO
updated 9.6 years ago by
Marc Carlson
★ 7.2k • written 9.6 years ago by
artur
▴ 80
4
votes
1
reply
8.6k
views
WGCNA-unable to install GO.db package
go
cancer
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
852108577
▴ 20
0
votes
2
replies
8.3k
views
conditional replace column values with values from a different column
GO
GO
updated 13.1 years ago by
Wolfgang Huber
★ 13k • written 13.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
17
replies
8.3k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 11.2 years ago by
James W. MacDonald
65k • written 11.2 years ago by
Kamila Naxerova
▴ 100
2
votes
2
replies
8.0k
views
package built under R version 3.1.0 warning
GO
GO
updated 10.5 years ago by
Marc Carlson
★ 7.2k • written 10.5 years ago by
Diego Diez
▴ 760
0
votes
2
replies
7.8k
views
replace a value in a matrix using index
GO
GO
updated 11.6 years ago by
James W. MacDonald
65k • written 11.6 years ago by
Mark B
▴ 20
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO
gage
goseq
KEGG
updated 9.5 years ago by
Gordon Smyth
50k • written 9.6 years ago by
Merienne Nicolas
▴ 120
0
votes
2
replies
7.0k
views
Remove batch effects from RNA-seq data using edgeR and sva/ComBat
GO
edgeR
GO
edgeR
updated 10.9 years ago by
Gordon Smyth
50k • written 10.9 years ago by
David O'Brien
▴ 10
2
votes
7
replies
6.6k
views
GO.db installation error
go
sqlite
updated 8.4 years ago by
Daniel Lai
• 0 • written 8.5 years ago by
predeus
• 0
0
votes
1
reply
6.3k
views
using BioMart to query UniProt identifiers
GO
biomaRt
GO
biomaRt
updated 13.1 years ago by
Steffen Durinck
▴ 540 • written 13.1 years ago by
Wolfgang RAFFELSBERGER
▴ 140
4
votes
1
reply
6.0k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
adR
▴ 30
0
votes
1
reply
5.9k
views
standard deviation from log to normal scale???
Annotation
GO
Annotation
GO
updated 17.4 years ago by
Wolfgang Huber
★ 13k • written 17.4 years ago by
Jesper Ryge
▴ 110
0
votes
12
replies
5.3k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray
GO
oligo
AnnotationForge
Microarray
GO
oligo
AnnotationForge
11.2 years ago
James W. MacDonald
65k
1
vote
1
reply
5.2k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 9.3 years ago by
Luo Weijun
★ 1.6k • written 9.3 years ago by
Alan Smith
▴ 150
0
votes
8
replies
5.2k
views
Error loading GO.db
Annotation
GO
Annotation
GO
updated 10.9 years ago by
Dan Tenenbaum
★ 8.2k • written 10.9 years ago by
Anne Deslattes Mays
▴ 30
2
votes
1
reply
5.2k
views
GO of clusterprofiler
go
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
doaa.mohamed
• 0
0
votes
2
replies
5.1k
views
Packages not getting installed
Microarray
GO
annotate
Microarray
GO
annotate
updated 15.0 years ago by
James W. MacDonald
65k • written 15.0 years ago by
Ashwin Kumar
▴ 90
0
votes
4
replies
5.0k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO
Category
goseq
GO
Category
goseq
updated 8.1 years ago by
darshinimamindla
▴ 10 • written 12.7 years ago by
Helen Wright
▴ 10
1
vote
2
replies
5.0k
views
biomaRt: getting start and end locations of gene on chromosome
GO
biomaRt
GO
biomaRt
updated 14.8 years ago by
James W. MacDonald
65k • written 14.8 years ago by
Tim Smith
★ 1.1k
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 12 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
5
votes
7
replies
4.9k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Jon Bråte
▴ 250
0
votes
3
replies
4.8k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 22 months ago by
pengmin.wang.1
• 0 • written 12.2 years ago by
Marc Carlson
★ 7.2k
4
votes
3
replies
4.8k
views
Use R/Bioconductor to match BLAST hits to GO terms?
GO
BLAST
annotation
updated 9.6 years ago by
Marc Carlson
★ 7.2k • written 9.6 years ago by
Jon Bråte
▴ 250
0
votes
8
replies
4.8k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
Guest User
★ 13k
0
votes
2
replies
4.7k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Polikepahad, Sumanth
▴ 10
0
votes
2
replies
4.4k
views
Annotate - gene name to ENSEMBL
Microarray
GO
lumi
Microarray
GO
lumi
updated 10.5 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 10.5 years ago by
Kripa R
▴ 180
0
votes
9
replies
4.4k
views
What does "level" argument mean in groupGO function (cluster profiler)?
clusterprofiler
go
groupGO
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
b.nota
▴ 360
0
votes
4
replies
4.2k
views
gsea (gene set enrichment analysis) for ranked lists
GO
GO
updated 13.0 years ago by
Luo Weijun
★ 1.6k • written 13.1 years ago by
Asta Laiho
▴ 120
0
votes
5
replies
4.2k
views
GSEA and edgeR
GO
edgeR
GO
edgeR
updated 12.7 years ago by
Gordon Smyth
50k • written 12.7 years ago by
Iain Gallagher
▴ 930
0
votes
10
replies
4.2k
views
GOStat and multiple testing
GO
GOstats
GO
GOstats
updated 19.8 years ago by
A.J. Rossini
▴ 810 • written 19.8 years ago by
Arne.Muller@aventis.com
▴ 620
1
vote
4
replies
4.1k
views
[topGO] More flexible way to select 'interesting' genes
GO
probe
topGO
GO
probe
topGO
updated 10.7 years ago by
Adrian Alexa
▴ 400 • written 10.7 years ago by
enricoferrero
▴ 660
0
votes
0
replies
4.0k
views
[R] object is not subsettable
GO
Cancer
annotate
GO
Cancer
annotate
17.2 years ago
Seth Falcon
★ 7.4k
0
votes
3
replies
4.0k
views
Openening qPCR file from ABI
GO
GO
updated 11.7 years ago by
Guido Hooiveld
★ 3.9k • written 11.7 years ago by
Guest User
★ 13k
3
votes
4
replies
3.9k
views
How to retrieve all GO terms at level 5 as well as their annotated genes
GO
GO
10.9 years ago
Peter Davidsen
▴ 210
0
votes
1
reply
3.9k
views
edgeR: common vs tagwise dispersion
GO
edgeR
GO
edgeR
14.0 years ago
Gordon Smyth
50k
0
votes
3
replies
3.9k
views
extracting topGO gene ids from result object
Annotation
GO
topGO
Annotation
GO
topGO
updated 13.4 years ago by
Valerie Obenchain
★ 6.8k • written 13.4 years ago by
Paul Rigor
▴ 110
0
votes
2
replies
3.9k
views
Gene filtering for RNA-seq data
Normalization
GO
Network
HTSFilter
DESeq2
Normalization
GO
Network
HTSFilter
DESeq2
updated 10.5 years ago by
Michael Love
41k • written 10.5 years ago by
Guest User
★ 13k
0
votes
2
replies
3.8k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 8.8 years ago by
marksteve952
• 0 • written 11.1 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
3.8k
views
Problems creating topGOdata object!
GO
topGO
GO
topGO
updated 12.6 years ago by
Valerie Obenchain
★ 6.8k • written 12.6 years ago by
gabriel teku
▴ 80
0
votes
10
replies
3.7k
views
problem while loading affycoretools
GO
GO
updated 10.6 years ago by
James W. MacDonald
65k • written 10.6 years ago by
Mayte Suarez-Farinas
▴ 510
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 6 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
1
reply
3.7k
views
rowttests() function in genefilter library
GO
GO
updated 14.4 years ago by
rgentleman
★ 5.5k • written 14.4 years ago by
Paul Geeleher
★ 1.3k
0
votes
1
reply
3.7k
views
goseq - overrepresented p-values
GO
Category
goseq
GO
Category
goseq
updated 12.9 years ago by
Alicia Oshlack
▴ 100 • written 12.9 years ago by
Gu Mi
▴ 30
1
vote
8
replies
3.7k
views
GRanges apply functions
GO
annotate
GO
annotate
updated 9.9 years ago by
Tim Triche
★ 4.2k • written 9.9 years ago by
Lescai, Francesco
▴ 380
0
votes
2
replies
3.7k
views
Single channel data analysis with LIMMA
GO
probe
limma
GO
probe
limma
updated 14.9 years ago by
Sean Davis
21k • written 14.9 years ago by
Marcel Dinger
▴ 20
3
votes
3
replies
3.6k
views
how to find ensembl genes belonging to a GO category?
biomart
gene ontology
GO
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
Guido Hooiveld
★ 3.9k
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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