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Question: How to get chip information from annotation databases
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gravatar for Agaz Hussain Wani
4 months ago by
India
Agaz Hussain Wani260 wrote:

I am interested to get the chip name of the annotation databases for example hgu133a.db. I get the following information when I enter the database name into the RStudio console.

> hgu133a.db
ChipDb object:
| DBSCHEMAVERSION: 2.1
| Db type: ChipDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMANCHIP_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| MANUFACTURER: Affymetrix
| CHIPNAME: Human Genome U133 Set
| MANUFACTURERURL: http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133
| EGSOURCEDATE: 2015-Sep27
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: ENTREZID
| TAXID: 9606
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 20150919
| GOEGSOURCEDATE: 2015-Sep27
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
| GPSOURCEURL: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19
| GPSOURCEDATE: 2010-Mar22
| ENSOURCEDATE: 2015-Jul16
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.uniprot.org/
| UPSOURCEDATE: Thu Oct  1 23:31:58 2015

 

I got database name by 

> hgu133a.db$packageName
[1] "hgu133a.db"

How can I get the chipname i,e Human Genome U133 Set

ADD COMMENTlink modified 4 months ago by Martin Morgan ♦♦ 22k • written 4 months ago by Agaz Hussain Wani260
2
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

metadata() returns the information about the chip; it's a data.frame so

> subset(metadata(hgu133a.db), name == "CHIPNAME", value)
                  value
8 Human Genome U133 Set

 

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 22k
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