That issue goes beyond the ImaGene format. When doing contact printing of microarrays it is still fairly common to spot the same probe 2 or more times as shown in the example here (http://www.digitalapoptosis.com/2005/10/12/dna-microarray/).
It is also very common for commercial arrays (Agilent for example) to have multiple copies of their control spots. We'll take a look at the Illumina plug-ins but I'm sure that there is a more elegant solution. What were are trying to do is, theoretically, simple since our data is already background-substracted and normalized (ImaGene does a perfectably acceptable job in doing that). We have two collums with ch1 and ch2 normalized intensities in Log2 and a Flag column showing spots that have to be filtered out. We were hoping to use BASE to help up organize our experiments before sending them off to MeV. In the Base2 demo server, the demoHyb1 bioassay is similar to our situation. When I open that item and click on the "Raw data" tab, It appears that the spot coordinate were imported and then used to produce columns entitled [Rep] Name and [Rep] ID that clearly come from duplicate spots. That's what we are trying to replicate. Thanks, On 2011-11-21, at 12:36 PM, Nicklas Nordborg wrote: > On 2011-11-21 17:08, Nantel Andre wrote: >> Greetings, >> >> We are currently trying to integrate BASE into our lab and writing the >> necessary plug-ins to import normalized data from ImaGene. Let's just >> say that the lack of documentation has been "challenging". >> >> Right now we are trying to figure out how to deal with duplicate spots. >> From the GenePix examples in the Base2 server we see cases of raw >> biosassays wtih [raw] columns defined by the unique spot coordinates as >> well as “rep‘ columns containing the duplicated GeneID classifiers. Any >> suggestions on how to do this? > > What do you mean with a duplicate spots? Physically a spot is a spot and > there can of course only be one on a given position. However there is > nothing in BASE that prevents two or more spots from referencing the > same gene/reporter. Then there are some platforms (for example Illumina > BeadArrays) that doesn't have spots in the classical meaning. In this > case one need to construct a unique "feature id" for each "spot > equivalent" that one wants to measure. In the Illumina case, the unique > ID is provided by the "Illumicode" column in the data files. This value > is then mapped to gene/reporter annotations via a BGX file, and the > importer is also calculating means, etc for all entries with the same > "Illumicode" value. See > http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina for more > information about how the Illumina platform has been implemented. > > I don't know what kind of data files that are generated by the ImaGene > platform, so it is hard to advice on exactly how to the same thing for > ImaGene. > > /Nicklas > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
