Thanks a lot Jim! JP- --On Tuesday, May 02, 2006 10:51 AM -0400 "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Hi Jianping, > > Jianping Jin wrote: >> Dear list: >> >> There is an issue that is not clear to me, even after I read >> "Description of gcrma package" and the on-line help. The default >> setting for "affinity.info" is NULL. Based on the description for the >> program it appears that NULL does not use apm (for PM probe), amm (MM >> probe), or index of your own data. Are the affinities calculated in >> just.gcrma based on "hgu95av2" data set or something else with >> affinity.info=NULL? > > The affinities are calculated based on the MM sequences, which are > extracted from the corresponding probe package. Since they are based on > the sequence of the probes, there is no reason to use an individual data > set. > > You _could_ compute the affinities for a particular chip and then save > that data somewhere so you wouldn't have to compute it every time you ran > gcrma, which is why you have the option of specifying the affinity.info. > In fact it was suggested at one time by Robert Gentleman that we should > put the affinity.info somewhere (I suggested the probe packages) so it > wouldn't have to be recomputed every time, which is simply a waste of > compute cycles. However, people got busy and it never got implemented. > >> >> Another question I have is for "type". As there is no default parameter >> for the type setting, which model does "just.gcrma" take for running >> without defining any parameters? > > There _is_ a default parameter. Any time you see something like > > type = c("fullmodel", "affinities", "mm", "constant") > > in the arguments of a function, there should be a corresponding > > type <- match.arg(type) > > in the body of the function. If you don't specify a type, then the > argument that will be matched by default is the first one in the argument > vector, which in this case is 'fullmodel'. > > HTH, > > Jim > > >> >> I will appreciate it if you could help me out! >> >> Jianping >> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> x Jianping Jin Ph.D. x >> x Bioinformatics scientist x >> x Center for bioinformatics x >> x 3133 Bioinformatics Building x >> x CB# 7104 x >> x University of North Carolina x >> x Chapel Hill, NC 27599 x >> x Tel: (919)843-6105 x >> x Fax: (919)843-3103 x >> x E-mail: jjin at email.unc.edu x >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> >> _______________________________________________ >> 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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx