BeadChip location info.
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Yu Chuan Tai ▴ 440
@yu-chuan-tai-1534
Last seen 10.2 years ago
Hi list, I am new to the Illumnia Sentrix Human-6 BeadChip and have a basic question which I didn't find an answer in the archive. Just want to know how I can get the chromosome location informationm for each bead type, if I have a txt file with all the ID_REF? Thanks! Yu Chuan
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Lynn Amon ▴ 110
@lynn-amon-1601
Last seen 10.2 years ago
I have deposited some annotation files for the Illumina Sentrix beadchips in Bioconductor (illuminaHumanv1 and illuminaHumanv2) which contain chromosome information. The probe identifiers are Illumina's target IDs. If you have a text file written out by the scanner with all the individual beads, you will need an annotation package with bead identifiers. I have those too but they are not on Bioconductor. I can send that if you like but the file size is large. Let me know what version your BeadChip is (v1 or v2) and what the ID_REFs look like and I'll tell you which annotation package you need. Lynn Amon Research Scientist University of Washington On Mon, 4 Jun 2007, Yu Chuan Tai wrote: > Hi list, > > I am new to the Illumnia Sentrix Human-6 BeadChip and have a basic > question which I didn't find an answer in the archive. Just want to know > how I can get the chromosome location informationm for each bead type, if > I have a txt file with all the ID_REF? > > Thanks! > Yu Chuan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks a lot for your help. What I have is actually a public database. The ID_REF look like GI_10047089-S, GI_10047133-A, GI_10047133-I, Hs.22815-S, hmm8932-S, lysA....etc. I am not sure if these are v1 or v2 because they didn't say. But there are 47293 bead types in total. I think before I get into any annotation package, I should ask the authors if they have the chr location info. already. I will keep you posted about this and let you know if I need anything from you. Best, Yu Chuan On Tue, 5 Jun 2007, Lynn M Amon wrote: > I have deposited some annotation files for the Illumina Sentrix beadchips in > Bioconductor (illuminaHumanv1 and illuminaHumanv2) which contain chromosome > information. The probe identifiers are Illumina's target IDs. If you have a > text file written out by the scanner with all the individual beads, you will > need an annotation package with bead identifiers. I have those too but they > are not on Bioconductor. I can send that if you like but the file size is > large. Let me know what version your BeadChip is (v1 or v2) and what the > ID_REFs look like and I'll tell you which annotation package you need. > > Lynn Amon > Research Scientist > University of Washington > > > > On Mon, 4 Jun 2007, Yu Chuan Tai wrote: > >> Hi list, >> >> I am new to the Illumnia Sentrix Human-6 BeadChip and have a basic >> question which I didn't find an answer in the archive. Just want to know >> how I can get the chromosome location informationm for each bead type, if >> I have a txt file with all the ID_REF? >> >> Thanks! >> Yu Chuan >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >
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The annotation packages on Bioconductor will work with these IDs. You have v1 so you need the illuminaHumanv1 package. Use the illuminaHumav1CHRLOC to get the chromosome locations. Lynn Yu Chuan Tai wrote: > Thanks a lot for your help. What I have is actually a public database. > The ID_REF look like GI_10047089-S, GI_10047133-A, GI_10047133-I, > Hs.22815-S, hmm8932-S, lysA....etc. I am not sure if these are v1 or > v2 because they didn't say. But there are 47293 bead types in total. > > I think before I get into any annotation package, I should ask the > authors if they have the chr location info. already. I will keep you > posted about this and let you know if I need anything from you. > > Best, > Yu Chuan > > On Tue, 5 Jun 2007, Lynn M Amon wrote: > >> I have deposited some annotation files for the Illumina Sentrix >> beadchips in Bioconductor (illuminaHumanv1 and illuminaHumanv2) which >> contain chromosome information. The probe identifiers are Illumina's >> target IDs. If you have a text file written out by the scanner with >> all the individual beads, you will need an annotation package with >> bead identifiers. I have those too but they are not on >> Bioconductor. I can send that if you like but the file size is >> large. Let me know what version your BeadChip is (v1 or v2) and what >> the ID_REFs look like and I'll tell you which annotation package you >> need. >> >> Lynn Amon >> Research Scientist >> University of Washington >> >> >> >> On Mon, 4 Jun 2007, Yu Chuan Tai wrote: >> >>> Hi list, >>> >>> I am new to the Illumnia Sentrix Human-6 BeadChip and have a basic >>> question which I didn't find an answer in the archive. Just want to >>> know >>> how I can get the chromosome location informationm for each bead >>> type, if >>> I have a txt file with all the ID_REF? >>> >>> Thanks! >>> Yu Chuan >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >>
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I see. Thanks!! Best, Yu Chuan On Tue, 5 Jun 2007, Lynn Amon wrote: > The annotation packages on Bioconductor will work with these IDs. You > have v1 so you need the illuminaHumanv1 package. Use the > illuminaHumav1CHRLOC to get the chromosome locations. > Lynn > > > Yu Chuan Tai wrote: >> Thanks a lot for your help. What I have is actually a public database. >> The ID_REF look like GI_10047089-S, GI_10047133-A, GI_10047133-I, >> Hs.22815-S, hmm8932-S, lysA....etc. I am not sure if these are v1 or >> v2 because they didn't say. But there are 47293 bead types in total. >> >> I think before I get into any annotation package, I should ask the >> authors if they have the chr location info. already. I will keep you >> posted about this and let you know if I need anything from you. >> >> Best, >> Yu Chuan >> >> On Tue, 5 Jun 2007, Lynn M Amon wrote: >> >>> I have deposited some annotation files for the Illumina Sentrix >>> beadchips in Bioconductor (illuminaHumanv1 and illuminaHumanv2) which >>> contain chromosome information. The probe identifiers are Illumina's >>> target IDs. If you have a text file written out by the scanner with >>> all the individual beads, you will need an annotation package with >>> bead identifiers. I have those too but they are not on >>> Bioconductor. I can send that if you like but the file size is >>> large. Let me know what version your BeadChip is (v1 or v2) and what >>> the ID_REFs look like and I'll tell you which annotation package you >>> need. >>> >>> Lynn Amon >>> Research Scientist >>> University of Washington >>> >>> >>> >>> On Mon, 4 Jun 2007, Yu Chuan Tai wrote: >>> >>>> Hi list, >>>> >>>> I am new to the Illumnia Sentrix Human-6 BeadChip and have a basic >>>> question which I didn't find an answer in the archive. Just want to >>>> know >>>> how I can get the chromosome location informationm for each bead >>>> type, if >>>> I have a txt file with all the ID_REF? >>>> >>>> Thanks! >>>> Yu Chuan >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Nianhua Li ▴ 70
@nianhua-li-2181
Last seen 10.2 years ago
Did you check the corresponding annotation packages? http://bioconductor.org/packages/2.0/IlluminaChip.html best Nianhua Li
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@keith-satterley-1452
Last seen 10.1 years ago
Australia
I've been creating a script to install all packages that I want on computers in our Institute and I've been checking what is installed by biocLite. The web page: http://www.bioconductor.org/docs/install-howto.html is incorrect. The error is that the page states that biocLite actually installs 20 packages, including reposTools. However, reposTools is not installed, but affyQCreport is installed. Could the install-howto be corrected? I guess to be technically correct, it could be pointed out on the web page that installing the packages using biocLite also causes dependent packages, widgetTools, affyio, GO, KEGG, tkWidgets, simpleaffy and RcolorBrewer to be installed as well. At least, this happens on my Windows XP installation of R2.5.0. cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia
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Hi Keith, Keith Satterley wrote: > I've been creating a script to install all packages that I want on computers in > our Institute and I've been checking what is installed by biocLite. > > The web page: > > http://www.bioconductor.org/docs/install-howto.html > > is incorrect. The error is that the page states that biocLite actually installs > 20 packages, including reposTools. However, reposTools is not installed, but > affyQCreport is installed. > > Could the install-howto be corrected? Done. Thanks for pointing this! > > I guess to be technically correct, it could be pointed out on the web page that > installing the packages using biocLite also causes dependent packages, > widgetTools, affyio, GO, KEGG, tkWidgets, simpleaffy and RcolorBrewer to be > installed as well. At least, this happens on my Windows XP installation of R2.5.0. Yes but as Seth mentioned, this list can change and there is probably little value to keep track of it in our install-howto webpage. Cheers, H. > > cheers, > > Keith > > ======================== > Keith Satterley > Bioinformatics Division > The Walter and Eliza Hall Institute of Medical Research > Parkville, Melbourne, > Victoria, Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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