Hi All, I have gene description of microarray in text file (not the GAL file as given for the swirl example in limma package) and the data set is also in the text file. As i undertsnad there are no facilities for importing marrayRaw objects into limma. I want to analyse the whole data in limma for the color flip experiments. I can import the data for analysis in limma package but have not been able to feed in the layout of my array. Please let me know how to do this. I have 2 "grid columns" and 12 "grid rows". Within each grid there are 45 "spot columns" and 21 "spot rows". Is there anythng similar to "widget.marrayLayout()" in limma package? Thanks in advance. Binita Dr. Binita Dutta MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium

At 09:09 PM 11/02/2004, Binita Dutta wrote: >Hi All, > >I have gene description of microarray in text file (not the GAL file as >given for the swirl example in limma package) and the data set is also in >the text file. As i undertsnad there are no facilities for importing >marrayRaw objects into limma. There are now. See the 'convert' package at http://bioinf.wehi.edu.au/limma/convert.html. This package will be added to Bioconductor soon, but you can download it from there in the meantime. > I want to analyse the whole data in limma for the color flip > experiments. I can import the data for analysis in limma package but have > not been able to feed in the layout of my array. Please let me know how > to do this. I have 2 "grid columns" and 12 "grid rows". Within each grid > there are 45 "spot columns" and 21 "spot rows". I agree that this is not as well documented now as it was in the past, since I simplified the commands in the User's Guide. You need layout=list(ngrid.r=2,ngrid.c=12,nspot.r=45,nspot.c=21). See help("PrintLayout-class"). > Is there anythng similar to "widget.marrayLayout()" in limma package? Not exactly, but there is as entire GUI interface to limma available at http://bioinf.wehi.edu.au/limmaGUI/. Gordon >Thanks in advance. > >Binita >Dr. Binita Dutta >MicroArray Facility(MAF) >UZ Gasthuisberg >Onderwijs en Navorsing >Herestraat 49 >3000 Leuven >Belgium > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor