[BioC] Annotation Database for Agilent 8x60K Human Gene Expression Arrays

[Marc Carlson]

Hi Karthik,

The 8x60 arrays have a different design ID so out of caution, I would 
not recommend that you use that package for this.  Even if all the IDs 
from the other design id are present here (and that is a big if), you 
may still in certain circumstances end up thinking that you tried to 
measure a bunch of things that you did not try to measure.  The design 
ID was put into the name to try and avoid this confusion and to warn you 
about possible inconsistencies.

Here is the page from Agilents website that gives the design IDs for the 
platforms in question along with links to their eArray web application 
that allows access to the files which they supply probe mappings for.

http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductData&PageID=1516

 From that eArray link you should be able to just download the file (one 
for the 8x60 arrays) and then just follow the directions from the 
SQLForge vignette from the AnnotationDbi package to make an annotation 
package for the 8x60 arrays.  It's pretty easy to make an annotation 
package.  The tricky part is usually getting the mapping information 
from the manufacturers, but it sounds like you have already done that part.

Here is where you can find that SQLForge vignette:

http://www.bioconductor.org/packages/2.10/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf


For more information about the Agi4x44PreProcess you should look at the 
vignette for that package here:

http://www.bioconductor.org/packages/2.10/bioc/vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf

The vignette certainly makes it seem like you can use this package with 
other Agilent annotations, but you might want to ask Pedro about exactly 
how accommodating his design is intended to be.

Hope this helps,


   Marc



On 06/18/2012 04:09 AM, Karthik K N wrote:
> Dear Members (and especially Marc Carlson),
>
> I have few questions:
>
> 1. I was wondering whether HsAgilentDesign026652.db is the latest updated
> database for Agilent 8x60K human gene expression arrays or is there any
> other file?  I have been told by Axel that HsAgilentDesign026652.db cover
> the oligos used by the Agilent 4x44Kv2 arrays, so I am not sure if I can
> use this for 8x60K arrays.
>
> 2. If I can indeed use HsAgilentDesign026652.db for 8x60K arrays, is it
> possible to use it as annotation file for Agi4x44PreProcess package so that
> I can use the same codes from this package to analyze 8x60K arrays?
>
> 3. If I want to create an annotation file to be used in any of the
> packages, what are the requirements (files, tools etc) for it? I have an
> annotation file in excel format given to me by my microarray service
> provider, so If I want to use that annotation file in Agi4x44Preprocess
> package (or any other package that requires this file) what should I do?
>
> Thanks a lot in advance for all your suggestions!
>
> Cheers,
>
> Karthik
>
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>
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