Thanks Mark for pointing out this. Regards, Stefano On Fri, Aug 25, 2006 at 04:04:47PM +0100, Mark Dunning wrote: <mark>So just to clarify, here is the situation regarding BeadArray raw data. <mark> <mark>If you have made the appropriate tweaks to the BeadScan software then <mark>you should get a text file that look like this (for each array/strip); <mark> <mark>Code Grn GrnX GrnY <mark>50008 796 536.5297 3167.486 <mark>50008 495 1574.66 12360.35 <mark>50008 706 2120.334 14611.3 <mark>50008 519 1493.311 17420.35 <mark>50008 938 1549.49 11478.03 <mark>50008 612 1989.498 4735.532 <mark>50008 744 1073.537 15349.49 <mark>.......... <mark> <mark>********************************************* <mark>For instructions on how to make the tweaks in BeadScan go to <mark> <mark>http://www.damtp.cam.ac.uk/user/npt22 <mark> <mark>On that page you will find an xml file to replace the existing <mark>Settings.xml file within the BeadScan program directory <mark> <mark>Note that these steps can only be used before scanning new arrays. I <mark>don't know of any way to recover the x and y coordinates for arrays <mark>that have been previously scanned. <mark> <mark> ********************************************* <mark> <mark> <mark>As Sean notes, each bead is identified by a Code and not a TargetID <mark>as seen in the BeadStudio output. This is annoying, but it is <mark>possible to match up the two identifiers using the bead set manifest <mark>that Illumina distributes on their cd's when they give the arrays <mark>(its a csv file). <mark> <mark> <mark>The Grn column gives the bead intensity that has been calculated <mark>using Illumina image processing methods which include a "sharpening" <mark>transformation and a local background correction. It is possible for <mark>both these steps to produce negative values. The beadarray package is <mark>able to use the TIF images and the X and Y coordinates from the text <mark>file to calculate bead intensities. It is possible to re-create the <mark>steps that Illumina use although we store the local foreground and <mark>background for each bead separately so that background correction is <mark>optional. We are also looking to implement a method of background <mark>estimation using morphological filtering. <mark> <mark>We have only just seen this new text format for ourselves, so the <mark>code to read these files is only available in the latest version of <mark>beadarray in the developers section. <mark> <mark>So in summary, with the Code, X and Y information plus the .tif <mark>image, you can re-create the Illumina image analysis yourself to get <mark>raw intensities at the probe level using the beadarray package. <mark>Currently this takes around 1min for each array (strip) i.e. about <mark>10-15mins for each chip [ 3Ghz machine with 3GB ram]. <mark> <mark>Hope this helps, <mark> <mark> <mark> <mark>Mark <mark> <mark>On 25 Aug 2006, at 14:55, Stefano Calza wrote: <mark> <mark>> <mark>> <mark>>On Fri, Aug 25, 2006 at 09:42:36AM -0400, Sean Davis wrote: <mark>><sean>Mark, <mark>><sean> <mark>><sean>Have you made any headway with Illumina regarding getting <mark>>data that is <mark>><sean>closer to "raw" but still useful? We are getting the probe- <mark>>level data <mark>><sean>dumped from our (which I think is NOT background- subtracted, <mark>>but correct me <mark>><sean>if I am wrong), but these data do not conform to the usual <mark>>Illumina output <mark>><sean>(different unique ids for the probes), so I really haven't <mark>>given much <mark>><sean>thought to using them, particularly since I can't convince <mark>>our collaborators <mark>><sean>to make hacks of their scanner config file to get the dumps <mark>>for all the data <mark>><sean>we receive. <mark>><sean> <mark>> <mark>> <mark>>I guess we are getting something like that, but afaik the dumps are <mark>>already somehow corrected (and I get some negative values). The <mark>>scanner itself may do some background correction when dumping numbers. <mark>>You may need to use the raw scanned image, but it may not be <mark>>possible (if not through an agreement with Illumia). <mark>> <mark>>I'm just trying to understand what's in this data, so correct me if <mark>>I'm wrong. <mark>> <mark>>Regards, <mark>>Stefano <mark>> <mark>>-- <mark>>Stefano Calza, PhD <mark>>Researcher - Biostatistician <mark>>Sezione di Statistica Medica e Biometria <mark>>Dipartimento di Scienze Biomediche e Biotecnologie <mark>>Universit? degli Studi di Brescia - Italy <mark>>Viale Europa, 11 25123 Brescia <mark>>email: calza at med.unibs.it <mark>>Phone: +390303717653 <mark>>Fax: +390303717488 <mark>> <mark>>_______________________________________________ <mark>>Bioconductor mailing list <mark>>Bioconductor at stat.math.ethz.ch <mark>>https://stat.ethz.ch/mailman/listinfo/bioconductor <mark>>Search the archives: http://news.gmane.org/ <mark>>gmane.science.biology.informatics.conductor <mark>> -- Stefano Calza, PhD Researcher - Biostatistician Sezione di Statistica Medica e Biometria Dipartimento di Scienze Biomediche e Biotecnologie Universit? degli Studi di Brescia - Italy Viale Europa, 11 25123 Brescia email: calza at med.unibs.it Phone: +390303717653 Fax: +390303717488