[BioC] hgu133_plus_2?

[James W. MacDonald]

Carl-Magnus Högerkorp wrote:
> Hi!
> 
> New to this list and to Bioconductor, I apologize if bringing up old
> matters, but I need a solution to my problem, which is:
> 
> When trying to load a set of 30 x (hgu133_plus_2) .cel files, this message
> pops up:
> 
> 
>>rawBcells<-ReadAffy()
> 
> Error: cannot allocate vector of size 317553 Kb
> In addition: Warning message:
> Reached total allocation of 1022Mb: see help(memory.size)
> 
> Obviously there is a shortage of memory as I interpret it.
> So, any suggestions on how I should address this, since I want to run gcrma,
> normalizations and clustering etc on this set?

You could try justGCRMA(), which uses much less memory. Alternatively 
you could purchase another Gig of RAM, which these days is very inexpensive.

> 
> The next problem arising is when trying to run separate files with gcrma:
> 
> 
>>raw0001<-ReadAffy("B cells P-00.01.CEL")
>>grma0001<-gcrma(raw0001)
> 
> Computing affinities.Done.
> Adjusting for optical effect.Done.
> Error in model.frame(formula, rownames, variables, varnames, extras,
> extranames,  :
>         variable lengths differ
> 
> is gcrma unable to read (hgu133_plus_2).cel files?
> The library for hgu133_plus_2 is loaded OK.

No, it is because you tried to run gcrma on only one chip. For any of 
the methods that model the probe-level data (gcrma, rma, affyPLM, 
li.wong), it doesn't make any sense to use only one chip, which is why 
you are erroring out. Try using maybe 4 or 5 chips and see what happens.

> 
> Thanks!
> 
> Carl-Magnus
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109