[BioC] problems with affy in unix

[feiwan]

Dear bioconductor users:

I encontoured two problems with affy in unix. the dataset is the Leukemia data from Stjude.org

Question1:
 
I tried to merge two big affybatch data sets in R (under unix mainframe) and encounter the problems as following:

combine2.3<-merge(combine2.1,TALL)
Error: cannot allocate vector of size 409600 Kb

Question2:

Affybatch BCR does not have names for each sample (only H). 

> > > setwd("/export/home/fwan/data/BCR")
BCR<-ReadAffy()> 
> BCR
AffyBatch object
size of arrays=640x640 features (51204 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=16
number of genes=12625
annotation=hgu95av2
> exprs(BCR)[1,]
   H    H    H    H    H    H    H    H    H    H    H    H    H    H    H    H 
 687  859  883  608  711  567  827  572  621  607  565  802 1292  583  683  659 
> 

Question3:

there 335 cel files and If R can not process all of them at the same time, can I break them into different groups and then run RMA on each group? I know the final expression values will be different but I do not know if it will have a big effects on final data analysis. 



I am very new to this area. any suggustion will be appreciated.

regards,

w.f 




	[[alternative HTML version deleted]]