Hi All, I have 200 CEL files and i want to use bioconductor to read these files and then do simple things like hist(),boxplot()! I think i will run into memory issues! Any suggestions as to how to handle this problem? Thanks in advance. Hrishi

Hrishikesh Deshmukh wrote: > Hi All, > > I have 200 CEL files and i want to use bioconductor to > read these files and then do simple things like > hist(),boxplot()! I think i will run into memory > issues! > Any suggestions as to how to handle this problem? If you want to have an AffyBatch so you can use hist(), etc., you will need lots of RAM (probably 3 or 4 Gb). You might also need to use a *nix OS because windows doesn't handle memory that efficiently. Luckily, RAM is comparatively cheap these days. Best, Jim > > Thanks in advance. > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Do you want to plot the data before or after preprocessing ? The current maximum features are 242 million (=55000x200x22) and 11 million (=55000x200). Also do you want to investigate the distribution of each array/column or look at overall distribution. With my Pentium 4 at 1.6 GHz and 512 RAM, I can do a hist() or boxplot() on the pre-processed dataset. mat <- matrix( rnorm(55000*200), nc=200 ) library(fields) system.time( bplot(mat) ) [1] 16.21 1.23 23.83 0.00 0.00 But the real problem is that there are too many data points on the graphs that makes each array difficult to see. I think it would be better to read in, say 25-50 arrays at a time and plot their distribution. Besides being less memory intensive, the graphics may look well spaces for you to look at. Regards, Adai On Tue, 2005-03-08 at 11:10 -0800, Hrishikesh Deshmukh wrote: > Hi All, > > I have 200 CEL files and i want to use bioconductor to > read these files and then do simple things like > hist(),boxplot()! I think i will run into memory > issues! > Any suggestions as to how to handle this problem? > > Thanks in advance. > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi, I once did RMA on 237 CEL files and needed about 5Gb RAM on a Linux machine to do this. Cheers, Steffen Hrishikesh Deshmukh wrote: >Hi All, > >I have 200 CEL files and i want to use bioconductor to >read these files and then do simple things like >hist(),boxplot()! I think i will run into memory >issues! >Any suggestions as to how to handle this problem? > >Thanks in advance. >Hrishi > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >