Dear All, I want to analyse my data in limmaGUI. We have our own chip and use agilent scanner to scan the slide. Later the scanned image is analysed by "Array vision" program. We export the data from Array vision as text file and then upload the text file in the database. With this set up, I want to know how I can analyse the data with limmaGUI. (It is possible to export the files from our database as text file). Best Regards, Binita One more question: can I import normalised M and A values from other program and then perform linear model fit using limma. ============================== Binita Dutta, PhD MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium

Hi Binita, On Tue, 31 Aug 2004, Binita Dutta wrote: > I want to analyse my data in limmaGUI. We have our own chip and use agilent > scanner to scan the slide. Later the scanned image is analysed by "Array > vision" program. We export the data from Array vision as text file and then > upload the text file in the database. limmaGUI should be able to read in ArrayVision files OK. Just follow the "Swirl" example in the documentation, replacing the SPOT files (listed in the Targets file) with ArrayVision files. > (It is possible to export the files from our database as text file). limmaGUI is not designed to interact directly with a database. You should use standard ArrayVision files (in tab-delimited text format), so if this requires exporting from your database, then do that, (but ensure that importing/exporting files into/out of database hasn't modified them from their original ArrayVision format). > With this set up, I want to know how I can analyse the data with limmaGUI. This question is too general. Please say whether you have attempted to read the limmaGUI documentation and run through examples, and where you have succeeded/failed using the example data set(s) e.g. Swirl, and whether you have succeeded/failed in reading in your own data into limmaGUI. > One more question: can I import normalised M and A values from other > program and then perform linear model fit using limma. Yes, certainly, but limma has plenty of good normalisation methods for two-colour arrays, so you might not need to. There is a feature in limmaGUI designed to input M and A values obtained from output from the former marrayTools (now part of marray). So if you can get your normalised M A data in this format, then you can use this feature. But it is easier to do the normalisation in limma/limmaGUI, unless you have a specific reason why you want to do normalisation elsewhere. Regards, James