We are still in the process of implementing GCRMA for the gene ST platforms and it is not yet included in the current version. Best, Jean Wu James MacDonald wrote: > Hi Sneha, > > There are going to be several problems for you. First, the getDataAffy() function expects the data to be in a certain format which is obviously being violated here. So you _could_ modify the probe_tab file to conform to that format. > > However, a bigger problem is that the chip you are using is a PM- only chip. There are some background probes on the chip, but they are not MM-probes so I don't believe the underlying assumptions for the gcrma model are going to apply. > > Best, > > Jim > > > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 >>>> sneha patil 01/28/10 2:04 AM >>> > hiii, > > i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a > probe package....while making the probe package i am getting this > error.....also my probe file is the zip file.,.... > >> makeProbePackage("Hugene-1_0-st-v1.r3",datafile = > gzfile("HuGene-1_0-st-v1.probe.tab",open="r"), > + outdir = "outdir",maintainer = "me",version = "0.0.1",species = > "Homo_sapiens", > + check = FALSE,force = TRUE) > Importing the data. > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > scan() expected 'an integer', got '+' > > > plzz help me regarding this > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > > _______________________________________________ > 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 -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu