Hi all. My name is AG LEE, a new bioconductor user. Our project is using HG_U133 plus 2 chips which contain approximately 56,000 probes and the .cel file in text format is about 32MB. Currently we have more than 100 chips and number is growing quickly. I tried to get the data into bioconductor using ReadAffy and can only read in 19 chips before it run out of memory (my machine has 1 GB memory). I tried to normalize the data using "expresso(d, normalize.method ="invariantset", bg.correct = FALSE, pmcorrect.method="pmonly", summary.method="liwong"" and it ran out of memory before the completion. I have option to upgrade my memory to 4GB, but still concern whether it will really help when our chips number reaches several hundres or thousands. Does anybody can help me with some suggestions? Thanks in advance. AG LEE [[alternative HTML version deleted]]

Right now, I am using Mac OS X 10.3.3 with 1.5 GB memory. I recently performed data preprocessing of HG_U133 Version 2. I was able to do RMA analysis up to 100 CEL files successfully. However, I was not able to do it for 150 CEL files, unfortunately. -_-;; (I think the job crashed around 130 CEL files, but I am not sure ...) If your machine has 1GB memory, I think the limit of CEL files you can do analysis must be around 60 or 70. Good luck! On Jun 29, 2004, at 2:53 PM, Li, Aiguo (NIH/NCI) wrote: > Hi all. > > My name is AG LEE, a new bioconductor user. Our project is using > HG_U133 > plus 2 chips which contain approximately 56,000 probes and the .cel > file in > text format is about 32MB. Currently we have more than 100 chips and > number > is growing quickly. I tried to get the data into bioconductor using > ReadAffy and can only read in 19 chips before it run out of memory (my > machine has 1 GB memory). I tried to normalize the data using > "expresso(d, > normalize.method ="invariantset", bg.correct = FALSE, > pmcorrect.method="pmonly", summary.method="liwong"" and it ran out of > memory > before the completion. I have option to upgrade my memory to 4GB, but > still > concern whether it will really help when our chips number reaches > several > hundres or thousands. > > Does anybody can help me with some suggestions? > > Thanks in advance. > > AG LEE > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724