Thanks, Ben. That helps a lot! But I still have some questions? Would you please also help me on this. > There were significant changes in the structure of the PLMset object > between 1.2.x and 1.3.x which is why you are having problems with the > boxplot(), Mbox() commands on your old PLMset using the new code. But why when I reload in to R 2.0.1 ( the on ei used to generate PLMset object), and tried boxplot ( suppose to produce NUSE plot), it gave me something strange (see attachment) > > To reduce memory usage with fitPLM I suggest that you do something like > the following > > Pset <- fitPLM(my.Data,output.param=list(varcov="none")) > > which should significantly reduce memory usage (and this should really > be the default setting, an oversight on my part which will be fixed > shortly). > > > Also, if you can live without the weights (or alternatively the > residuals) you could do > > Pset <- fitPLM(my.Data,output.param=list(varcov="none",weights=FALSE)) > > > or > > Pset <- fitPLM(my.Data,output.param=list(varcov="none",residuals=FALSE)) > > which would also reduce the memory overhead. Will those simplificaiton change the underlying model that is fitted to the data. e.g., weights=FALSE doesn't this mean it won't use iteratively reweighted least squares (IRLS)? Thanks! Fangxin > On Thu, 2005-06-09 at 10:22 -0700, fhong at salk.edu wrote: >> Sorry to bring such an old question up again. I hope that somebody can >> explain what is happening here. >> >> (1) >> I tried to run fitPLM to about 72 affy ATH1 arrays. It worked with >> affyPLM >> version 1.2.5 under R2.0.1, then I saved it as "dataPLM.RData" with >> option >> "compress=TRUE" >> Later when I reload "dataPLM.RData" into working space (R2.1.0) and try >> to >> run boxplot and Mbox, it told me that >> >> " Error in if (object at model.description$R.model$which.parameter.types[3] >> == >> : >> argument is of length zero >> since object at model.description is NULL." >> >> How did this happen? Does "compress=TRUE" destroy some of the internal >> structure of PLMset object? >> >> (2) >> then I tried to run fitPLM again ( on the affyBatch object I saved >> before) >> using package affyPLM version 1.3.3 under R2.1.0 But this time it >> wouldn't >> finish (after Background correcting PM, Normalizing PM) >> but generated an error of R and closed R after that. I thought that may >> because my laptop has only 1.5Gb memory. >> Does this mean that there is some substantial change of affyPLM package >> between version 1.3.3 and version 1.2.5? >> >> >> I then tried to run this using a Linux machine with 4Gb accessible >> memory >> size (there is no limitation in memory for each user and I reboot the >> system as a super user). But I still got the error message about memory, >> saying >> >> > Pset.Goda=fitPLM(data.Goda.I) >> Background correcting PM >> Normalizing PM >> Fitting models >> Error: cannot allocate vector of size 52 Kb >> >> Does this mean 4Gb is still not enough? >> >> My last question is what I need to update my computer in order to >> analyze >> 72 arrays together (simpleaffy, affyPLM,Limma...) >> >> >> Thank you very much, any suggestion will be highly appreciated! >> Fangxin >> >> >> >> >> -------------------- >> Fangxin Hong Ph.D. >> Plant Biology Laboratory >> The Salk Institute >> 10010 N. Torrey Pines Rd. >> La Jolla, CA 92037 >> E-mail: fhong at salk.edu >> (Phone): 858-453-4100 ext 1105 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > -- > Ben Bolstad <bolstad at="" stat.berkeley.edu=""> > http://www.stat.berkeley.edu/~bolstad > > > -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105