[BioC] BeadChip location info.

Lynn Amon lynnamon at u.washington.edu
Tue Jun 5 18:51:43 CEST 2007

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. 

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
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