[BioC] memory problem with fitPLM in package affyPLM

[fhong at salk.edu]

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