Dear Wolfgang and Bioconductor people, I am using the combineAffyBatch function from the matchprobes package regularly now, and I am very pleased with its performance. However, I was wondering if you can help me with the following: I understand that every time I run the function, a new .CDF object is created and this takes a considerable amount of time. I was wondering if we can re-use an existing "newcdf" object when performing new analysis where the same two types of arrays are used. In other words, since I am always combining the same 2 types Affy chips, the newcdf object should be the same. If I use that object from previous sessions, I shouldn't be creating a new one every time. I would greatly appreciate it if you could tell me if that is feasible, and if it is, how can I do it. Thank you very much for your attention to this issue. Cathy -- Catherine Dumur, Ph.D. Assistant Professor Department of Pathology Virginia Commonwealth University Clinical Support Center, 2nd floor, room 247 403 North 13th Street Richmond, VA 23298-0248 Phone: (804) 828-9564 or Direct: (804) 828-2800 ext. 106 Fax: (804) 225-4738

Hi Catherine, Catherine Dumur wrote: > Dear Wolfgang and Bioconductor people, > > I am using the combineAffyBatch function from the matchprobes package > regularly now, and I am very pleased with its performance. > > However, I was wondering if you can help me with the following: > > I understand that every time I run the function, a new .CDF object is > created and this takes a considerable amount of time. I was wondering if > we can re-use an existing "newcdf" object when performing new analysis > where the same two types of arrays are used. In other words, since I am > always combining the same 2 types Affy chips, the newcdf object should > be the same. If I use that object from previous sessions, I shouldn't be > creating a new one every time. You are correct, you _shouldn't_ be creating a new one every time. Instead, you should save() the newcdf object and load() it back in when you need it. An example would be: save(newcdf, file="newcdf.Rda") load("newcdf.Rda") If you use this newcdf regularly, you might even want to build a data package. See 'Writing R Extensions' for more information. HTH, Jim > > I would greatly appreciate it if you could tell me if that is feasible, > and if it is, how can I do it. > > Thank you very much for your attention to this issue. > > > Cathy > -- 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.

Dear Catherine it is feasible to do this, you will have to modify the combineAffyBatch function to do this (do you know how to find its source code?). If you like, your modifications would be welcome to be fed back into the package. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > I am using the combineAffyBatch function from the matchprobes package > regularly now, and I am very pleased with its performance. > > However, I was wondering if you can help me with the following: > > I understand that every time I run the function, a new .CDF object is > created and this takes a considerable amount of time. I was wondering if > we can re-use an existing "newcdf" object when performing new analysis > where the same two types of arrays are used. In other words, since I am > always combining the same 2 types Affy chips, the newcdf object should > be the same. If I use that object from previous sessions, I shouldn't be > creating a new one every time. > > I would greatly appreciate it if you could tell me if that is feasible, > and if it is, how can I do it. > > Thank you very much for your attention to this issue. > > > Cathy >