Showing : organism • reset
0
votes
8
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2.0k
views
AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 17.4 years ago by ▴ 190 • written 17.4 years ago by ★ 2.9k
0
votes
10
replies
2.8k
views
gene set enrichment
Annotation Organism Annotation Organism
updated 2.1 years ago by 50k • written 11.4 years ago by ▴ 220
0
votes
4
replies
1.7k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.2 years ago delhomme@embl.de ★ 1.2k
0
votes
7
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1.5k
views
I have trouble running the AnnBuilder Vignette
Cancer Organism AnnBuilder Cancer Organism AnnBuilder
updated 19.5 years ago by 65k • written 19.5 years ago by ★ 2.0k
0
votes
4
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1.3k
views
Annotation data package is not being created
Annotation Organism PROcess Annotation Organism PROcess
updated 20.4 years ago by ★ 2.9k • written 20.4 years ago by ▴ 70
0
votes
4
replies
1.3k
views
cluster a set of genes based on another set of genes
Organism limma Organism limma
updated 17.2 years ago by ▴ 280 • written 17.2 years ago by ▴ 450
0
votes
7
replies
1.6k
views
annotation package for chicken affyprobes
Annotation Organism Gallus gallus probe AnnBuilder Annotation Organism Gallus gallus probe
updated 17.7 years ago by ▴ 180 • written 17.7 years ago by ▴ 870
0
votes
3
replies
2.6k
views
GOStats: summary hyperGTest, count and size
Annotation GO Organism GOstats Annotation GO Organism GOstats
10.1 years ago Christine Gläßer ▴ 60
0
votes
4
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1.8k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
11.5 years ago Ricardo Silva ▴ 110
0
votes
4
replies
1.3k
views
Error while using AnnBuilder
Annotation GO Organism annotate AnnBuilder Annotation GO Organism annotate AnnBuilder
updated 18.2 years ago by ★ 7.4k • written 18.2 years ago by ▴ 160
0
votes
6
replies
1.5k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures genomes Cancer Organism biomaRt GenomicFeatures
updated 12.1 years ago by ▴ 660 • written 12.1 years ago by 16k
0
votes
3
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1.5k
views
AnnBuilder/ABPkgBuilder: lots of Errors
Annotation GO Cancer Organism Biobase annotate AnnBuilder PROcess bridge Annotation GO
updated 19.6 years ago by ★ 2.9k • written 19.6 years ago by ▴ 90
0
votes
6
replies
1.5k
views
adding environment variables
Organism Organism
updated 13.5 years ago by ▴ 10 • written 13.5 years ago by ▴ 280
0
votes
4
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1.0k
views
ABPkgBuilder Error; Again: Solved
Annotation GO Cancer Organism Biobase annotate AnnBuilder PROcess Annotation GO Cancer
updated 18.7 years ago by ★ 7.4k • written 18.7 years ago by ▴ 250
0
votes
6
replies
1.3k
views
Making use of the Apis mellifera assembly 2 data in goSeq
GO Organism Apis mellifera goseq GO Organism Apis mellifera goseq
updated 12.2 years ago by 16k • written 12.2 years ago by ▴ 30
0
votes
5
replies
1.4k
views
AnnBuilder problem with custom List of genes
Annotation Organism probe AnnBuilder Annotation Organism probe AnnBuilder
16.7 years ago claudio.is@libero.it ▴ 210
0
votes
7
replies
913
views
advantages of annotation packages
Annotation GO Organism Annotation GO Organism
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 30
0
votes
3
replies
830
views
Finding Annotation of CEL file formats
Organism probe Organism probe
updated 15.6 years ago by ★ 3.9k • written 15.6 years ago by ▴ 230
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votes
3
replies
1.2k
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
10.7 years ago Sashi ▴ 20
0
votes
2
replies
1.8k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation
updated 9.0 years ago by ▴ 20 • written 10.3 years ago by ▴ 40
0
votes
7
replies
1.9k
views
Gene Ontology Annotations from Gene Names
Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats
updated 10.2 years ago by 65k • written 10.2 years ago by ★ 13k
0
votes
2
replies
2.4k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ★ 13k
0
votes
2
replies
855
views
AnnBuilder problem?
Organism Biobase annotate AnnBuilder Organism Biobase annotate AnnBuilder
updated 18.5 years ago by ▴ 780 • written 18.5 years ago by ▴ 50
0
votes
4
replies
4.3k
views
An error in oligo: All the CEL files must be of the same type??
BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism
updated 12.9 years ago by ★ 4.3k • written 12.9 years ago by ▴ 20
0
votes
2
replies
1.5k
views
KEGGgraph, error
Organism hgu133a KEGGgraph Organism hgu133a KEGGgraph
updated 15.0 years ago by ▴ 20 • written 15.0 years ago by ▴ 380
0
votes
4
replies
1.2k
views
Creating annotation package with a new database schema
Annotation GO Organism Annotation GO Organism
updated 11.5 years ago by 16k • written 11.5 years ago by ▴ 30
0
votes
3
replies
1.0k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures Cancer Organism biomaRt GenomicFeatures
updated 12.2 years ago by ▴ 660 • written 12.2 years ago by ★ 1.6k
0
votes
2
replies
1.4k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.7 years ago by ▴ 150 • written 12.7 years ago by ▴ 380
0
votes
2
replies
2.4k
views
Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!
Organism limma SPIA Organism limma SPIA
updated 12.3 years ago by ▴ 570 • written 12.3 years ago by ▴ 100
2
votes
4
replies
2.7k
views
makePdInfoPackage for Primeview arrays
BiocViews Annotation Cancer Organism cdf probe affy biocViews BiocViews BiocViews Cancer
updated 10.9 years ago by ★ 3.9k • written 10.9 years ago by ▴ 140
0
votes
4
replies
1.0k
views
missing AnnBuilder parser
Annotation Organism annotate AnnBuilder Annotation Organism annotate AnnBuilder
updated 19.0 years ago by ★ 2.9k • written 19.1 years ago by ★ 1.3k
0
votes
3
replies
1.2k
views
Building the tomato annotation library(Affy)
Annotation Organism AnnBuilder Annotation Organism AnnBuilder
17.0 years ago Groot, Philip de ▴ 630
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votes
6
replies
1.3k
views
org.*.eg.db problem
Annotation Organism Annotation Organism
updated 13.4 years ago by 6.7k • written 13.4 years ago by ▴ 200
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votes
2
replies
814
views
GO and Annotation
Annotation GO Organism Annotation GO Organism
updated 20.0 years ago by 65k • written 20.0 years ago by ▴ 300
0
votes
2
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2.5k
views
annotation and GO for non-model organism
Microarray Annotation GO Organism Microarray Annotation GO Organism
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 150
0
votes
3
replies
1.1k
views
error in gene2pathway results
Organism gene2pathway Organism gene2pathway
updated 14.1 years ago by ★ 7.2k • written 14.1 years ago by ▴ 420
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votes
5
replies
1.2k
views
Arabidopsis chromosome location mappings
Organism ath1121501 Organism ath1121501
updated 15.6 years ago by ▴ 10 • written 15.6 years ago by ▴ 330
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votes
2
replies
1.1k
views
AnnBuilder problem
Organism annotate AnnBuilder Organism annotate AnnBuilder
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 130
0
votes
3
replies
824
views
AnnBuilder URL error.
GO Organism AnnBuilder GO Organism AnnBuilder
updated 19.2 years ago by 65k • written 19.2 years ago by ▴ 540
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votes
4
replies
8.1k
views
DESeq adjusted pvalue calculation / filtering data
Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq
updated 12.4 years ago by ★ 6.0k • written 12.4 years ago by ▴ 20
0
votes
5
replies
1.6k
views
newbie problems with AnnBuilder
Annotation Organism cdf probe affy AnnBuilder Annotation Organism cdf probe affy
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 830
0
votes
3
replies
1.4k
views
RpsiXML issues with latest Biogrid release files
GO Organism Arabidopsis thaliana graph RpsiXML GO Organism Arabidopsis thaliana graph
updated 14.4 years ago by ▴ 340 • written 14.4 years ago by ▴ 60
0
votes
3
replies
1.4k
views
find overlaping genes in ENSEMBL gene ID list and NCBI gene ID list
Organism Bos taurus Organism Bos taurus
updated 13.1 years ago by ★ 7.2k • written 13.1 years ago by ▴ 150
0
votes
3
replies
1.5k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
0
votes
1
reply
988
views
bug in resourcerer2BioC in Resourcerer package
Organism Resourcerer Organism Resourcerer
updated 19.4 years ago by ★ 2.9k • written 19.4 years ago by ★ 1.3k
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
1
reply
846
views
AnnBuilder error
GO Organism annotate AnnBuilder GO Organism annotate AnnBuilder
updated 18.2 years ago by ▴ 780 • written 18.2 years ago by ▴ 510
0
votes
3
replies
1.7k
views
Fwd: Re: which package can do GSEA for no model organism
Annotation GO Organism ASSIGN Annotation GO Organism ASSIGN
updated 14.8 years ago by ▴ 40 • written 14.8 years ago by ▴ 340
0
votes
1
reply
696
views
Error with AnnBuilder ABPkgBuilder
GO Organism annotate AnnBuilder GO Organism annotate AnnBuilder
updated 18.3 years ago by ▴ 780 • written 18.3 years ago by ▴ 20
0
votes
2
replies
1.3k
views
GO over representation analysis
Annotation Pathways GO Organism db0 AnnBuilder PROcess maanova AnnotationDbi Annotation
updated 15.7 years ago by ▴ 220 • written 15.7 years ago by ★ 7.2k
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?
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