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How can I find the annotation file of Human HT-12 v2 BeadChip?
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Posted by
Kev Go
How can I find the annotation file of Human HT-12 v2 BeadChip?
Had a similar problem lately, got in touch with Illumina tech support but with no luck. Ended up using Ensembl REST API to download associations starting from rs codes, if you've a minimum skill in programming it should not be too difficult!
Had a similar problem lately, got in touch with Illumina tech support but with no luck. Ended up using Ensembl REST API to download associations starting from rs codes, if you've a minimum skill in programming it should not be too difficult!
The Illumina technical support team replied HT-12v2 array product does not exist in their catalog. The HT-12 chip was marketed as a version 3 at launch and there is no previous version.
The Illumina technical support team replied HT-12v2 array product does not exist in their catalog. The HT-12 chip was marketed as a version 3 at launch and there is no previous version.
Thanks a lot for the answers. I searched in both GEO and Bioconductor, only could find annotation data of platform "Illumina human-6 v2.0 expression beadchip" with manufacturer name "illuminaHumanv2". There are only 4 versions in Illumina expression beadchip: "Illumina human-6 v1.0 expression beadchip" "GPL6097" "illuminaHumanv1" "Illumina human-6 v2.0 expression beadchip" "GPL6102" "illuminaHumanv2" "Illumina HumanHT-12 V3.0 expression beadchip" "GPL6947" "illuminaHumanv3" "Illumina HumanHT-12 V4.0 expression beadchip" "GPL10558" "illuminaHumanv4" I think "illuminaHumanv2" is the annotation file should be used.
Thanks a lot for the answers. I searched in both GEO and Bioconductor, only could find annotation data of platform "Illumina human-6 v2.0 expression beadchip" with manufacturer name "illuminaHumanv2". There are only 4 versions in Illumina expression beadchip: "Illumina human-6 v1.0 expression beadchip" "GPL6097" "illuminaHumanv1" "Illumina human-6 v2.0 expression beadchip" "GPL6102" "illuminaHumanv2" "Illumina HumanHT-12 V3.0 expression beadchip" "GPL6947" "illuminaHumanv3" "Illumina HumanHT-12 V4.0 expression beadchip" "GPL10558" "illuminaHumanv4" I think "illuminaHumanv2" is the annotation file should be used.
Had a similar problem lately, got in touch with Illumina tech support but with no luck. Ended up using Ensembl REST API to download associations starting from rs codes, if you've a minimum skill in programming it should not be too difficult!
Had a similar problem lately, got in touch with Illumina tech support but with no luck. Ended up using Ensembl REST API to download associations starting from rs codes, if you've a minimum skill in programming it should not be too difficult!
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http://www.bioconductor.org/help/search/index.html?q=HumanHT-12
searching in bioconductor for the acronym name HumanHT-12, or sometimes a simplified version, ex HumanHT12. The actual useful packages will be of type hgu133a2probe, hgu133a2cdf, hgu133a2.db. For Affymetrix, there should be one of each: [AnnotDbiPkgRoot]probe, [AnnotDbiPkgRoot]cdf, [AnnotDbiPkgRoot].db
A list of packages can be seen in AnnotationDBI webpage http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html.
http://www.bioconductor.org/help/search/index.html?q=HumanHT-12
searching in bioconductor for the acronym name HumanHT-12, or sometimes a simplified version, ex HumanHT12. The actual useful packages will be of type hgu133a2probe, hgu133a2cdf, hgu133a2.db. For Affymetrix, there should be one of each: [AnnotDbiPkgRoot]probe, [AnnotDbiPkgRoot]cdf, [AnnotDbiPkgRoot].db
A list of packages can be seen in AnnotationDBI webpage http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html.
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The Illumina technical support team replied HT-12v2 array product does not exist in their catalog. The HT-12 chip was marketed as a version 3 at launch and there is no previous version.
The Illumina technical support team replied HT-12v2 array product does not exist in their catalog. The HT-12 chip was marketed as a version 3 at launch and there is no previous version.
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Thanks a lot for the answers. I searched in both GEO and Bioconductor, only could find annotation data of platform "Illumina human-6 v2.0 expression beadchip" with manufacturer name "illuminaHumanv2". There are only 4 versions in Illumina expression beadchip:
"Illumina human-6 v1.0 expression beadchip" "GPL6097" "illuminaHumanv1"
"Illumina human-6 v2.0 expression beadchip" "GPL6102" "illuminaHumanv2"
"Illumina HumanHT-12 V3.0 expression beadchip" "GPL6947" "illuminaHumanv3"
"Illumina HumanHT-12 V4.0 expression beadchip" "GPL10558" "illuminaHumanv4"
I think "illuminaHumanv2" is the annotation file should be used.
Thanks a lot for the answers. I searched in both GEO and Bioconductor, only could find annotation data of platform "Illumina human-6 v2.0 expression beadchip" with manufacturer name "illuminaHumanv2". There are only 4 versions in Illumina expression beadchip:
"Illumina human-6 v1.0 expression beadchip" "GPL6097" "illuminaHumanv1"
"Illumina human-6 v2.0 expression beadchip" "GPL6102" "illuminaHumanv2"
"Illumina HumanHT-12 V3.0 expression beadchip" "GPL6947" "illuminaHumanv3"
"Illumina HumanHT-12 V4.0 expression beadchip" "GPL10558" "illuminaHumanv4"
I think "illuminaHumanv2" is the annotation file should be used.
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I would have thought GEO would have basic platform information which you could download, otherwise I am certain it is in Bioconductor.
I would have thought GEO would have basic platform information which you could download, otherwise I am certain it is in Bioconductor.
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Hi,dear Peng
Did you find GPL10558 annotation package file?
I can't find it .
Hi,dear Peng
Did you find GPL10558 annotation package file?
I can't find it .
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