Hi, I would like to use my own set of negative control probes with gcrma. I can't find an example or explanation with the format of the NCprobe index file in the function description or gcrma instructions. Is it just a file with the x and y coordinates in columns? Does the bg.adjust.gcrma function read the file directly, or do I need to read the file first and create an object? Thanks for any help. Best, Hans van Leeuwen

The NCprobe is a vector of indexes for control probes. For example, let "object" be your AffyBatch or oligo object, if you do intensity(object)[NCprobe,] you will get the intensities of the control probes. You may need function "xy2i" to get the index if you start from the x and y coordinates of your control probes. best, Jean Wu On Wed, 28 Mar 2007, Hans van Leeuwen wrote: > Hi, > > I would like to use my own set of negative control probes with gcrma. I > can't find an example or explanation with the format of the NCprobe index > file in the function description or gcrma instructions. > > Is it just a file with the x and y coordinates in columns? Does the > bg.adjust.gcrma function read the file directly, or do I need to read the > file first and create an object? > > Thanks for any help. > > Best, > > Hans van Leeuwen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >