a good write up for affy chips is here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/se/lu/thep/affymetrix/README it kinda skips the initial setup part and goes right into analysis..
for genepix, I usually just use the gpr file.. but you can store the other files if you want to.. 1. zip up everything into a .zip file 2. import all the files using the zip plugin importer 3. create your biosources.. this will depend upon what kind of experiment you are doing we do ChIP-chip so we set up one biosource for chromatin, and one for the immunoppt antibody 4. make samples from your biosources 5. for ChIP-chip we make a pooled sample of the chromatin sample and the antibody sample as the experimental.. and just the chromatin sample as the input DNA.. 6. create labelled samples 7. make a hybridization, add the array slide.. if you havn't done so before.. you need to create your array platform.. this requires the GAL file so that you can import the reporters.. then you make an array batch.. then specific slides.. (see steps 2 and 3 from the affy readme) 8. make a scan from your hybridization 9. make a rawbioassay from your scan 10. import the data from your gpr file into the rawbioassay.. (using simple import plugin) 11. follow steps 4 and 5 of the affy README to make the experiment and the root bioassay set.. 12. after you have the root bioassay set, there will be some analysis icons where you can normalize the data and run other plugins.. i havn't done much analysis with BASE2 as i use various R packages.. -keith Gabe Dagani wrote: > Greetings, > > Has anyone created a simple walkthru for setting up a simple experiment, > uploading GPR, GPS, TIFF files into a project and doing some analysis? > > I am just a beginner and the manual is outdated for base 2.0. > > thanks - Gabe > > -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653 [EMAIL PROTECTED] 858-822-5767 ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
