Showing : AnnotationForge • reset
1
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22
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4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 7.3 years ago by ▴ 10 • written 7.7 years ago by • 0
0
votes
5
replies
2.0k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
9.3 years ago • updated 9.2 years ago oliver.tills • 0
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.8 years ago by ★ 1.0k • written 9.2 years ago by • 0
0
votes
4
replies
2.3k
views
IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
annotationforge
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ★ 3.7k
2
votes
28
replies
4.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 4 months ago by 65k • written 16 months ago by ▴ 10
3
votes
6
replies
946
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
10 months ago abhisek001 • 0
0
votes
14
replies
4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.2 years ago • updated 20 months ago Jenny Drnevich ★ 2.0k
3
votes
6
replies
2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.2 years ago MOD • 0
0
votes
2
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1.2k
views
makeOrgPackage: possible to add option to allow GO terms now in GO.db?
annotationforge makeorgpackage go
8.9 years ago Keith Hughitt ▴ 180
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
2
votes
4
replies
992
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
2
replies
1.6k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
1
vote
4
replies
2.7k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 8.3 years ago by ★ 6.8k • written 8.3 years ago by • 0
0
votes
3
replies
1.3k
views
error while making database using Annotationforge package
annotationforge error database
updated 7.8 years ago by ★ 3.9k • written 7.8 years ago by ▴ 10
2
votes
5
replies
755
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 6 months ago by 65k • written 6 months ago by ▴ 70
1
vote
3
replies
1.1k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
4
votes
5
replies
1.9k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
1
reply
1.7k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 10.8 years ago by 65k • written 10.8 years ago by ▴ 90
0
votes
1
reply
1.0k
views
an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 50
0
votes
1
reply
1.1k
views
答复: an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
10.7 years ago joseph ▴ 50
1
vote
3
replies
1.7k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 220
0
votes
1
reply
1.4k
views
Error using makeDBPackage() from AnnotationForge package
Annotation probe AnnotationForge Annotation probe AnnotationForge
updated 10.6 years ago by ★ 7.2k • written 10.6 years ago by ▴ 80
1
vote
1
reply
1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 80
3
votes
3
replies
8.6k
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 ★ 7.2k • written 9.6 years ago by ▴ 80
1
vote
2
replies
2.1k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb annotationdbi annotationforge
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ▴ 80
0
votes
3
replies
1.3k
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
5
replies
1.4k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 3.0 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
1
reply
514
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
15 months ago Mistinrain ▴ 10
1
vote
15
replies
2.2k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
15 months ago • updated 13 months ago Mistinrain ▴ 10
0
votes
7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.0 years ago by • 0 • written 2.5 years ago by • 0
4
votes
2
replies
4.1k
views
Install package without updating dependent package
Install AnnotationForge
2.4 years ago 亮 • 0
2
votes
4
replies
684
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
6 months ago Adrian • 0
0
votes
3
replies
739
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
5
replies
229
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 2 days ago by 65k • written 4 days ago by • 0
0
votes
1
reply
1.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
3
votes
7
replies
2.6k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.0 years ago by 65k • written 7.0 years ago by • 0
0
votes
10
replies
1.5k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
6.8 years ago gabciamm • 0
0
votes
1
reply
1.3k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 6.4 years ago by 65k • written 6.4 years ago by • 0
2
votes
2
replies
1.1k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 6.0 years ago by ★ 3.9k • written 6.0 years ago by • 0
1
vote
3
replies
1.3k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 20
1
vote
7
replies
1.4k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
votes
7
replies
1.8k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
0
votes
2
replies
798
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
2
replies
1.1k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
5
votes
7
replies
1.7k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 12 months ago by ▴ 50 • written 4.1 years ago by ▴ 20
0
votes
4
replies
933
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
1
vote
1
reply
1.3k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
3
votes
3
replies
755
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.0 years ago Marcelo Laia ▴ 450
0
votes
0
replies
1.1k
views
create custom 'System Biology' annotation package - class not found
AnnotationDb annotationdbi AnnotationForge
7.2 years ago Laure Cougnaud ▴ 20
0
votes
1
reply
475
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 15 months ago by • 0 • written 15 months ago by ▴ 10
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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
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I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
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