I have followed Jim's advice ( http://thread.gmane.org/gmane.science.biology.informatics.conductor/18 959/focus=18963) and built, without error messages, the pdInfo package for Affy Rat Gene ST. Now I am stuck. I've read the oligo vignette and it doesn't really address non-SNP arrays, particularly how to make an affyBatch for further processing. Can someone point me to the relevant info? Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]

Hi Mark, Mark Kimpel wrote: > I have followed Jim's advice ( > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 18959/focus=18963) > and built, without error messages, the pdInfo package for Affy Rat > Gene > ST. Now I am stuck. I've read the oligo vignette and it doesn't really > address non-SNP arrays, particularly how to make an affyBatch for further > processing. Can someone point me to the relevant info? ?read.celfiles ?rma Note that there isn't an AffyBatch class in oligo. You will be using an ExpressionSet for raw data and an ExonFeatureSet for the expression values. Best, Jim > Mark > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." -- B. > F. Skinner > ****************************************************************** > > [[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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662