Sorry for the stupid question, I'm totally a baginner in cDNA data Analysis... Can I derive the number of wells in a plate from a .gpr file ? I would like to use it for the normalization... I looked in the web and in the mailing list archives, with no big results... Thanks a lot Giulio...

Hi, no, a GenePix Result (GPR) file does not contain any information about the microtiter plates used for spotting. I've seen some labs adding plate information to the GenePix Array List (GAL) file, and then it was just the plate number (not the plate well coordinate). Such details are not required and there is no well defined name for it. I think this goes under optional "User Defined" column. You can read more about the different GenePix file formats on http://www.moleculardevices.com/pages/software/gn_genepix_file_formats .html. However, if the array has been spotted in a known order, say, from left to right top to bottom and you know if a 96 or 384 plate has been used, you can make an "intelligent guess" from where the spot originates. I did some of this a few years ago and the code is in the aroma package (http://www.braju.com/R/). A good start would be to look at the help for PlateGroups and PrintdipGroups (dip not tip) in that package. plotPrintdipOrder() and plotPrintorder() are also useful. Hope this help you get started Cheers Henrik On 3/17/06, Giulio Di Giovanni <perimessaggini at="" hotmail.com=""> wrote: > > Sorry for the stupid question, I'm totally a baginner in cDNA data > Analysis... > Can I derive the number of wells in a plate from a .gpr file ? > I would like to use it for the normalization... > > I looked in the web and in the mailing list archives, with no big results... > > Thanks a lot > > Giulio... > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >