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go
•
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9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.3 years ago by
Bernd Klaus
▴ 610 • written 9.3 years ago by
nw328
▴ 20
0
votes
3
replies
9.8k
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
66k • written 14.6 years ago by
Massimo Pinto
▴ 390
0
votes
2
replies
9.0k
views
Clusterprofiler error: No gene can be mapped
software error
go
annotation
clusterProfiler
updated 13 months ago by
tarltonuk2089
• 0 • written 4.1 years ago by
tianshenbio
• 0
4
votes
1
reply
8.7k
views
WGCNA-unable to install GO.db package
go
cancer
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
852108577
▴ 20
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 9.7 years ago by
Marc Carlson
★ 7.2k • written 9.7 years ago by
artur
▴ 80
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
66k • 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
66k • 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 9.6 years ago by
Gordon Smyth
50k • written 9.7 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 11.0 years ago by
Gordon Smyth
50k • written 11.0 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
6.4k
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
6.1k
views
Warning message as converting gene Symbol to ENTREZID
go
clusterprofiler
updated 3.9 years ago by
James W. MacDonald
66k • written 3.9 years ago by
adR
▴ 30
0
votes
1
reply
6.0k
views
standard deviation from log to normal scale???
Annotation
GO
Annotation
GO
updated 17.5 years ago by
Wolfgang Huber
★ 13k • written 17.5 years ago by
Jesper Ryge
▴ 110
0
votes
12
replies
5.4k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray
GO
oligo
AnnotationForge
Microarray
GO
oligo
AnnotationForge
11.3 years ago
James W. MacDonald
66k
1
vote
1
reply
5.3k
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
2
votes
1
reply
5.3k
views
GO of clusterprofiler
go
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
doaa.mohamed
• 0
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 11.0 years ago by
Anne Deslattes Mays
▴ 30
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
66k • written 15.0 years ago by
Ashwin Kumar
▴ 90
3
votes
11
replies
5.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 3.3 years ago by
Alberto
• 0
1
vote
2
replies
5.0k
views
biomaRt: getting start and end locations of gene on chromosome
GO
biomaRt
GO
biomaRt
updated 14.9 years ago by
James W. MacDonald
66k • written 14.9 years ago by
Tim Smith
★ 1.1k
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
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
4.9k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 23 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 10.2 years ago by
Steve Lianoglou
★ 13k • written 10.2 years ago by
Guest User
★ 13k
0
votes
2
replies
4.8k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.3 years ago by
Wolfgang Huber
★ 13k • written 12.3 years ago by
Polikepahad, Sumanth
▴ 10
0
votes
9
replies
4.4k
views
What does "level" argument mean in groupGO function (cluster profiler)?
clusterprofiler
go
groupGO
updated 6.1 years ago by
James W. MacDonald
66k • written 6.1 years ago by
b.nota
▴ 360
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
4
replies
4.2k
views
gsea (gene set enrichment analysis) for ranked lists
GO
GO
updated 13.1 years ago by
Luo Weijun
★ 1.6k • written 13.1 years ago by
Asta Laiho
▴ 120
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
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
1
vote
4
replies
4.1k
views
[topGO] More flexible way to select 'interesting' genes
GO
probe
topGO
GO
probe
topGO
updated 10.8 years ago by
Adrian Alexa
▴ 400 • written 10.8 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 11.8 years ago by
Guido Hooiveld
★ 4.0k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
3.9k
views
edgeR: common vs tagwise dispersion
GO
edgeR
GO
edgeR
14.1 years ago
Gordon Smyth
50k
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
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
42k • 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 8.9 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 12.7 years ago by
Valerie Obenchain
★ 6.8k • written 12.7 years ago by
gabriel teku
▴ 80
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 8 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
10
replies
3.8k
views
problem while loading affycoretools
GO
GO
updated 10.7 years ago by
James W. MacDonald
66k • written 10.7 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
1
reply
3.8k
views
rowttests() function in genefilter library
GO
GO
updated 14.5 years ago by
rgentleman
★ 5.5k • written 14.5 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
3.7k
views
how to find ensembl genes belonging to a GO category?
biomart
gene ontology
GO
updated 5.6 years ago by
James W. MacDonald
66k • written 5.6 years ago by
Guido Hooiveld
★ 4.0k
50 results • Page
1 of 1
Recent ...
Replies
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
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3.9k
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After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
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Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
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