[BioC] hgu133_plus_2?

[Sean Davis]

Carl-Magnus,

Does justGCRMA work for you?  I don't use it, but my understanding is 
that it helps to deal with some of the memory issues with the multistep 
solution.  The answers you get are the same, again, as I understand it. 
  Others may have more to say on the matter.

Sean

On Jan 25, 2005, at 9:26 AM, 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?
>
> 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.
>
> Thanks!
>
> Carl-Magnus
>
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