I have a couple of questions concerning the marrayRaw widget. First, when I create an marrayLayout object and specify a "*.gal" file containing info on spots and clones, and just type ">objectname", I get some summary information on the object. In this summary it is stated that I have a number of control spots, including 3xSSC, the Arab gene, and duplicates of each spot. Where does this information come from? Second, Is this information about control spots used in the normalization process? (I have used the maLormLoess() function). I'd be happy if someone could explain this to me. Regards, Niklas Nordquist

Hi Niklas, On Tue, 4 Jun 2002, Niklas Nordquist wrote: > I have a couple of questions concerning the marrayRaw widget. > First, when I create an marrayLayout object and specify a "*.gal" file > containing info on spots and clones, and just type ">objectname", I get > some summary information on the object. In this summary it is stated > that I have a number of control spots, including 3xSSC, the Arab gene, > and duplicates of each spot. Where does this information come from? This information was stored in your .gal file. Once you select an Info file (say myfile.gal) in the marrayLayout widget and click on GetInfo, a new widget opens up asking you to select the column which holds the control information in myfile.gal. You must have selected one of the myfile.gal columns when reading the data into R. > Second, Is this information about control spots used in the > normalization process? (I have used the maLormLoess() function). It's used only if you tell the normalization function to do so. For example, when using maNorm, the argument "subset" can be used to specify which spots to use in the normalization. Best, Sandrine > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >