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GO
•
reset
15
votes
18
replies
3.3k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Raito92
▴ 60
0
votes
17
replies
8.2k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 11.1 years ago by
James W. MacDonald
65k • written 11.1 years ago by
Kamila Naxerova
▴ 100
0
votes
14
replies
1.5k
views
GO's to gene's
GO
GO
updated 14.2 years ago by
Marc Carlson
★ 7.2k • written 14.2 years ago by
Loren Engrav
★ 1.0k
0
votes
13
replies
1.8k
views
Analysis affymetrix of experiment....help please
GO
GO
updated 11.6 years ago by
Sean Davis
21k • written 11.6 years ago by
suparna mitra
▴ 290
0
votes
13
replies
3.3k
views
DESeq and number of replicates required for RNA-Seq
GO
DESeq
GO
DESeq
updated 13.9 years ago by
Naomi Altman
★ 6.0k • written 13.9 years ago by
michael watson IAH-C
★ 3.4k
0
votes
13
replies
2.2k
views
Hypergeometric test with Disease Ontology
GO
hgu95av2
GO
hgu95av2
updated 13.3 years ago by
Gilbert Feng
▴ 300 • written 13.3 years ago by
Ted Morrow
▴ 60
0
votes
13
replies
2.3k
views
How to plot NGS data?
GO
BSgenome
geneplotter
PROcess
BSgenome
genomes
GO
BSgenome
geneplotter
PROcess
genomes
updated 12.2 years ago by
Martin Morgan
25k • written 12.2 years ago by
Bernd Jagla
▴ 30
0
votes
13
replies
2.8k
views
EnrichGO not working with db created from annotationhub
clusterProfiler
AnnotationHubData
GO
updated 23 months ago by
Guido Hooiveld
★ 3.9k • written 23 months ago by
Lucía
▴ 10
0
votes
12
replies
2.0k
views
Quick start to linking GO terms and microarray data
Microarray
GO
affy
PROcess
goTools
GOstats
Microarray
GO
affy
PROcess
goTools
GOstats
18.2 years ago
michael watson IAH-C
★ 3.4k
0
votes
12
replies
3.2k
views
testing GO categories with Fisher's exact test.
GO
Category
GO
Category
updated 20.2 years ago by
James W. MacDonald
65k • written 20.2 years ago by
Nicholas Lewin-Koh
▴ 430
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
0
votes
12
replies
2.0k
views
Building BioC 2.2 with R 2.7.0
GO
annaffy
simpleaffy
GO
annaffy
simpleaffy
updated 15.9 years ago by
Groot, Philip de
▴ 630 • written 15.9 years ago by
Atro Tossavainen
▴ 160
0
votes
12
replies
3.4k
views
Understanding limma, fdr and topTable
Microarray
GO
limma
Microarray
GO
limma
updated 15.8 years ago by
Robson, Samuel
▴ 10 • written 15.8 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
0
votes
12
replies
1.9k
views
Some Genefilter questions
GO
Survival
cdf
genefilter
geneplotter
tkWidgets
affy
affydata
widgetTools
gcrma
affyPLM
updated 17.4 years ago by
rgentleman
★ 5.5k • written 17.4 years ago by
Amy Mikhail
▴ 460
0
votes
11
replies
3.0k
views
Very low P-values in limma
miRNA
Microarray
Normalization
GO
vsn
limma
microRNA
miRNA
Microarray
Normalization
GO
updated 14.5 years ago by
Paul Geeleher
★ 1.3k • written 14.5 years ago by
Gordon Smyth
50k
0
votes
11
replies
1.7k
views
'recursive default argument' error in GOENTREZID2GO
GO
Biobase
genefilter
graph
Category
GO
Biobase
genefilter
graph
Category
updated 16.9 years ago by
Seth Falcon
★ 7.4k • written 16.9 years ago by
Oleg Sklyar
▴ 260
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
2
votes
11
replies
3.1k
views
R gives error when trying to install EnsDb.Hsapiens.v75 package
go
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
desara.gora
• 0
0
votes
11
replies
2.7k
views
trouble hacking plotPCA
GO
Survival
Biobase
genefilter
affy
affydata
graph
limma
gcrma
matchprobes
affyPLM
RBGL
updated 17.4 years ago by
Rustici, Gabriella NIH/NCI [F]
▴ 10 • written 17.4 years ago by
Jenny Drnevich
★ 2.2k
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma
mroast
GSEA
GO
illumina human ht-12 v4
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 830
0
votes
11
replies
1.8k
views
GOstats and GenePix arrays
GO
GOstats
GO
GOstats
18.0 years ago
Jacob Michaelson
▴ 320
0
votes
10
replies
1.9k
views
microRNA: which genes code for a specific mirna?
miRNA
GO
microRNA
miRNA
GO
microRNA
updated 14.1 years ago by
Cei Abreu-Goodger
▴ 830 • written 14.1 years ago by
Tim Smith
★ 1.1k
0
votes
10
replies
1.9k
views
comparing GO lists
Annotation
GO
Cancer
graph
GOstats
Annotation
GO
Cancer
graph
GOstats
updated 16.8 years ago by
Ana Conesa
▴ 130 • written 16.8 years ago by
rgentleman
★ 5.5k
0
votes
10
replies
2.1k
views
dealing with NAs in limma
GO
GO
updated 16.9 years ago by
Gordon Smyth
50k • written 16.9 years ago by
Francois Pepin
★ 1.3k
0
votes
10
replies
2.1k
views
Retrieve Entrez IDs for enriched GO terms
Microarray
Annotation
GO
limma
GOstats
biomaRt
Microarray
Annotation
GO
limma
GOstats
updated 14.6 years ago by
Heidi Dvinge
★ 2.0k • written 14.6 years ago by
Yuan Hao
▴ 90
0
votes
10
replies
4.1k
views
GOStat and multiple testing
GO
GOstats
GO
GOstats
updated 19.7 years ago by
A.J. Rossini
▴ 810 • written 19.7 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
10
replies
2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray
Annotation
GO
Network
Regression
Survival
Infrastructure
Escherichia coli
ROC
11.1 years ago
Julie Zhu
★ 4.3k
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
0
votes
10
replies
1.9k
views
Kegg Profile package problem
GO
KEGGprofile
GO
KEGGprofile
11.3 years ago
gregory voisin
▴ 430
0
votes
10
replies
1.7k
views
Read single channel GenePix in limma [was: Analyze miRNA experiment in Bioconductor]
miRNA
Microarray
Normalization
GO
limma
miRNA
Microarray
Normalization
GO
limma
updated 16.0 years ago by
Paul Geeleher
★ 1.3k • written 16.0 years ago by
Gordon Smyth
50k
0
votes
10
replies
1.7k
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO
Cancer
GOstats
affycoretools
GO
Cancer
GOstats
affycoretools
updated 16.6 years ago by
Jenny Drnevich
★ 2.2k • written 16.6 years ago by
Seth Falcon
★ 7.4k
0
votes
9
replies
1.8k
views
problem with duplicateCorrelation and ExpressionSet objects
GO
Survival
cdf
Biobase
graph
limma
gcrma
annaffy
affyPLM
simpleaffy
biomaRt
Category
updated 16.9 years ago by
Seth Falcon
★ 7.4k • written 17.0 years ago by
Jenny Drnevich
★ 2.2k
0
votes
9
replies
1.8k
views
ontoCompare (goTools) : goidvect error
GO
goTools
GO
goTools
12.7 years ago
Oana VIGY
▴ 80
0
votes
9
replies
1.6k
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
3.8 years ago
camillab.
▴ 10
0
votes
9
replies
1.8k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO
biomartr
annotation
ensemble
fungi
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Bettina
• 0
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.6 years ago
artur
▴ 80
0
votes
9
replies
4.3k
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
9
replies
1.6k
views
How are GO2PROBE built
GO
probe
AnnBuilder
GO
probe
AnnBuilder
updated 15.6 years ago by
Sean Davis
21k • written 15.6 years ago by
Oura Tomonori
▴ 30
0
votes
9
replies
1.7k
views
GO over representation analysis
Annotation
GO
maanova
Annotation
GO
maanova
updated 15.7 years ago by
Marc Carlson
★ 7.2k • written 15.7 years ago by
Heike Pospisil
▴ 310
0
votes
9
replies
2.6k
views
frma and alternative CDFs
GO
cdf
frma
BRAIN
GO
cdf
frma
BRAIN
updated 9.8 years ago by
Matthew McCall
▴ 830 • written 9.8 years ago by
Guest User
★ 13k
0
votes
9
replies
1.7k
views
problem with hyperGTest and ath1121501?
GO
GO
updated 17.5 years ago by
Seth Falcon
★ 7.4k • written 17.5 years ago by
Martin Olivier
▴ 70
0
votes
9
replies
2.0k
views
Extract genes for a GO term in GOstat
GO
GO
updated 13.9 years ago by
Chao-Jen Wong
▴ 580 • written 13.9 years ago by
Rohit Farmer
▴ 170
0
votes
9
replies
1.2k
views
Help with 'annotation' in GOHyeprGParamsClass
Annotation
GO
Yeast
Category
Annotation
GO
Yeast
Category
updated 15.5 years ago by
rgentleman
★ 5.5k • written 15.5 years ago by
Jason Myers
▴ 50
0
votes
9
replies
1.6k
views
specifications for exonmap database config file?
GO
exonmap
GO
exonmap
updated 15.4 years ago by
Heidi Dvinge
★ 2.0k • written 15.4 years ago by
Joseph Fass
▴ 70
0
votes
9
replies
1.6k
views
problem with GO terms
GO
GOstats
Category
GO
GOstats
Category
updated 12.4 years ago by
James W. MacDonald
65k • written 12.4 years ago by
Ina Hoeschele
▴ 620
7
votes
9
replies
3.0k
views
GSEABase - View/extract GO terms mapped to each GOslim
go
GSEABase
GOslim
gene ontology
4.2 years ago • updated 13 months ago
samwhite
▴ 20
0
votes
8
replies
1.4k
views
two-line labels in GO graphs
GO
graph
GO
graph
updated 16.1 years ago by
Marc Carlson
★ 7.2k • written 16.1 years ago by
Robert Castelo
★ 3.3k
0
votes
8
replies
2.0k
views
IPI to entrez id
Proteomics
GO
biomaRt
Proteomics
GO
biomaRt
13.1 years ago
Dick Beyer
★ 1.4k
0
votes
8
replies
1.5k
views
Unable to Generate QC Report for mogene10stv1
GO
affyQCReport
GO
affyQCReport
updated 13.4 years ago by
James W. MacDonald
65k • written 13.4 years ago by
Rick Frausto
▴ 110
0
votes
8
replies
1.3k
views
problem with getGOOntology
GO
GO
updated 19.1 years ago by
Sean Davis
21k • written 19.1 years ago by
Sean Cory
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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