Showing : annaffy • reset
3
votes
1
reply
1.1k
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
1
vote
10
replies
2.7k
views
Error installing Annaffy
affy annaffy go.db kegg.db
updated 7.0 years ago by 65k • written 7.0 years ago by • 0
0
votes
5
replies
2.6k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 9.8 years ago by ▴ 160 • written 9.9 years ago by 65k
0
votes
1
reply
1.5k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 10.3 years ago by 65k • written 10.3 years ago by ★ 13k
0
votes
2
replies
1.2k
views
Possible problem with Rhesus array annotation package
Annotation GO annotate annaffy Annotation GO annotate annaffy
updated 12.8 years ago by ★ 7.2k • written 12.8 years ago by ▴ 30
0
votes
1
reply
1.7k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 13.4 years ago by 25k • written 13.4 years ago by ▴ 20
0
votes
2
replies
1.0k
views
list of annaffy .db files?
Annotation annotate annaffy Annotation annotate annaffy
updated 13.7 years ago by 6.7k • written 13.7 years ago by ▴ 80
0
votes
1
reply
935
views
help with multtest and annaffy
annaffy annaffy
updated 13.9 years ago by 65k • written 13.9 years ago by ▴ 90
0
votes
2
replies
1.2k
views
help with illumina microarray (DASL)
Microarray Annotation annaffy lumi Microarray Annotation annaffy lumi
updated 13.9 years ago by ★ 1.2k • written 14.0 years ago by ▴ 90
0
votes
3
replies
1.4k
views
help with annaffy package
GO annaffy GO annaffy
14.0 years ago Taylor, Katie ▴ 90
0
votes
1
reply
1.2k
views
annaffy-like HTML autput for org.Hs.eg.db and similar metadata packages
Microarray Annotation GO annaffy Microarray Annotation GO annaffy
updated 14.0 years ago by 6.7k • written 14.0 years ago by ▴ 40
0
votes
3
replies
1.2k
views
annotation of affymetrix microarray data
annotate annaffy annotate annaffy
updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 90
0
votes
1
reply
902
views
Multiple genes per probeset
Annotation Cancer mouse4302 annaffy ASSIGN Annotation Cancer mouse4302 annaffy ASSIGN
updated 14.0 years ago by 65k • written 14.0 years ago by ★ 2.0k
0
votes
2
replies
1.3k
views
probe to entrezID mapping with aafLocusLink
GO hgu133plus2 probe annaffy convert GO hgu133plus2 probe annaffy convert
updated 14.4 years ago by 65k • written 14.4 years ago by ▴ 10
0
votes
7
replies
1.7k
views
Missing GeneSymbol and Name information in TopTable
Annotation hgu133plus2 annaffy affylmGUI Annotation hgu133plus2 annaffy affylmGUI
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
14.8 years ago James W. MacDonald 65k
0
votes
1
reply
934
views
problem with the structure of a list of pathways
Genetics Pathways probe annaffy Genetics Pathways probe annaffy
updated 14.9 years ago by 65k • written 14.9 years ago by ▴ 60
0
votes
0
replies
733
views
problem with annaffy package
annaffy annaffy
14.9 years ago Alberto Goldoni ▴ 420
0
votes
0
replies
946
views
problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
14.9 years ago Georg Otto ▴ 510
0
votes
5
replies
1.2k
views
annotation information about ecoli2
Annotation GO probe annaffy Annotation GO probe annaffy
updated 15.5 years ago by 65k • written 15.5 years ago by ▴ 10
0
votes
2
replies
4.0k
views
Human Gene 1.0 ST array
Annotation probe annaffy Annotation probe annaffy
updated 15.6 years ago by 65k • written 15.6 years ago by ▴ 10
0
votes
5
replies
5.0k
views
Affymetrix probeset ids to gene symbols
annaffy annaffy
updated 15.8 years ago by ▴ 160 • written 15.8 years ago by ▴ 300
0
votes
0
replies
1.1k
views
affycoretools vennSelect problem
Annotation GO Survival probe annotate genefilter affy graph limma gcrma annaffy RBGL
15.8 years ago Nick Henriquez ▴ 20
0
votes
2
replies
1.2k
views
affycoretools vennSelect problem
GO Survival annotate genefilter affy graph gcrma annaffy RBGL GOstats biomaRt affyio
updated 15.8 years ago by 65k • written 15.8 years ago by ▴ 30
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 ▴ 630 • written 15.9 years ago by ▴ 160
0
votes
0
replies
831
views
annaffy w/yeast2
yeast2 annaffy yeast2 annaffy
16.0 years ago Sebastien Gerega ▴ 370
0
votes
0
replies
1.2k
views
BioConductor Developer Workshop Lausanne 2008 Info
SNP Annotation annaffy AnnBuilder biomaRt cellHTS2 SNP Annotation annaffy AnnBuilder
16.2 years ago Darlene Goldstein ▴ 230
0
votes
2
replies
1.2k
views
getURL in annaffy fails when object length==1 (or how to cope with collapsed lists, arrays, etc?)
annaffy annaffy
updated 16.2 years ago by ▴ 540 • written 16.2 years ago by ▴ 30
0
votes
0
replies
1.1k
views
MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
16.5 years ago Boel Brynedal ▴ 200
0
votes
1
reply
755
views
OMIM and annaffy
affy annaffy affy annaffy
updated 16.7 years ago by 65k • written 16.7 years ago by ▴ 510
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 ★ 7.4k • written 17.0 years ago by ★ 2.2k
0
votes
1
reply
754
views
error in annaffy
annaffy annaffy
updated 17.0 years ago by 65k • written 17.0 years ago by ▴ 510
0
votes
0
replies
1.1k
views
RBGL: bfs & dfs with directed graphs
GO Biobase annotate geneplotter graph Rgraphviz annaffy RBGL convert GO Biobase graph
17.0 years ago stephen edwards ▴ 10
0
votes
2
replies
1.6k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.1 years ago by 50k • written 17.1 years ago by ▴ 680
0
votes
1
reply
1.1k
views
topTable "resort.by" broken...
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy
updated 17.1 years ago by 50k • written 17.1 years ago by ★ 2.2k
0
votes
1
reply
1.4k
views
question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
0
votes
1
reply
1.0k
views
amigo links: gene ontology annotation for probes
Annotation GO Biobase annotate annaffy Annotation GO Biobase annotate annaffy
updated 17.2 years ago by ▴ 10 • written 17.2 years ago by ▴ 220
0
votes
1
reply
1.2k
views
annaffy errors
GO Survival mgu74av2 cdf annotate affy limma gcrma matchprobes annaffy simpleaffy plier
updated 17.2 years ago by 65k • written 17.2 years ago by ▴ 320
0
votes
1
reply
1.1k
views
Problems with BioConductor 1.9 in R-2.4.1
annaffy annaffy
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 630
0
votes
2
replies
1.0k
views
2fold sigchanges from limma
GO Survival hgu133a2 annotate hexbin limma gcrma matchprobes annaffy GO Survival hexbin
updated 17.4 years ago by 50k • written 17.4 years ago by ▴ 60
0
votes
1
reply
877
views
Annaffy problem loading metadata
mouse4302 annaffy mouse4302 annaffy
18.0 years ago Bornman, Daniel M ▴ 110
0
votes
2
replies
1.1k
views
AnnBuilder problem for mu11ksuba
Organism mu11ksuba annotate limma gcrma matchprobes annaffy AnnBuilder Organism mu11ksuba
updated 18.1 years ago by ▴ 780 • written 18.1 years ago by ★ 1.4k
0
votes
4
replies
1.4k
views
coerce aafTable object into dataframe (annaffy)
annaffy annaffy
18.2 years ago Georg Otto ▴ 510
0
votes
1
reply
887
views
rbind in annaffy problem
GO hgu95av2 rat2302 cdf annotate affy graph annaffy RBGL GOstats biomaRt GO hgu95av2
updated 18.4 years ago by 65k • written 18.4 years ago by ▴ 890
0
votes
2
replies
1.1k
views
problem with annaffy aafFunction function
GO hgu95av2 rat2302 Biobase annotate reposTools affy annaffy GO hgu95av2 rat2302 affy
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 890
0
votes
4
replies
968
views
GO package
annaffy annaffy
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ▴ 490
0
votes
6
replies
1.4k
views
Many missing GO terms from GOHyperG call using mgu74av2
GO Survival hgu95av2 mgu74av2 Ruuid annotate multtest affy graph annaffy RBGL GOstats
updated 18.8 years ago by ★ 7.4k • written 18.8 years ago by ★ 1.4k
0
votes
3
replies
1.0k
views
misnamed annotation environments with annaffy
Annotation annaffy Annotation annaffy
updated 18.9 years ago by ★ 7.4k • written 18.9 years ago by ▴ 320
0
votes
1
reply
990
views
annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
18.9 years ago Yanqin Yang ▴ 250
0
votes
0
replies
831
views
annotation problem with hgu133plus2
GO cdf annotate reposTools affy siggenes annaffy GO cdf annotate reposTools affy
18.9 years ago Seth Falcon ★ 7.4k
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
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
WEHI, Melbourne, Australia, 1 minute ago
EMBL Heidelberg, 14 minutes ago
France, 17 minutes ago
France, 17 minutes ago
United States, 20 minutes ago
Traffic: 1084 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6