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 [[alternative HTML version deleted]]

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=Produc t&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/Agi4x44PrePro cess/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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor