[BioC] BeadChip location info.
Yu Chuan Tai
yuchuan at stat.Berkeley.EDU
Tue Jun 5 19:09:45 CEST 2007
I see. Thanks!!
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.
> 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.
>> 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
>>> 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
>>>> how I can get the chromosome location informationm for each bead
>>>> type, if
>>>> I have a txt file with all the ID_REF?
>>>> Yu Chuan
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> Search the archives:
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor