[BioC] problems with affy in unix

[James MacDonald]

1. You don't have enough memory to merge the two. 335 cel files will
take a TON of memory to deal with.

2. No idea on this one. What are the names of the cel files?

3. If you are just going to do RMA, then you could use justRMA instead.
You may have enough memory to do it, because this function is much less
memory intensive.

HTH,

Jim



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

>>> "feiwan" <wanf at email.uc.edu> 07/18/03 11:41PM >>>
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 




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