[BioC] hgu133_plus_2?

[marcus]

I guess that you can try something like:

>memory.limit(size=1500)

or whatever size you like. If you have a slow computer and a lot of
data, you might have to wait for a long long time..  :)



Marcus Gry Björklund
 
Royal Institute of Technology
AlbaNova University Center 
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

Phone (office): +46 8 553 783 44
Fax: + 46 8 553 784 81
Visiting address: Roslagstullsbacken 21, Floor 3
Delivery address: Roslagsvägen 30B                          
Web: http://www.biotech.kth.se/molbio/microarray/index.html

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Carl-Magnus
Högerkorp
Sent: Tuesday, January 25, 2005 15:26
To: Bioconductor
Subject: [BioC] hgu133_plus_2?

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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