[BioC] memory usage ReadAffy() and probe level information

Roel Verhaak r.verhaak at erasmusmc.nl
Tue Apr 6 14:32:10 CEST 2004


I have two questions regarding the use of the affy package:
- I have a large series of cel-files and am trying to read
them at once. Unfortunately, the ReadAffy-function seems to
use a lot of memory. My workstation has 2 Gig of RAM
installed, but trying to read >100 cel-files (HGU133a) is a
no-go. This is R1.8.1 with Bioconductor 1.3 on a Windows
machine. Reading in 50 cel-files already means a
(peak-)memory usage of 800 meg. Is there any solution to
this, because I would like to read 300 cel-files at the same
time if possible. I have played around with the
memory.limit()-function, but with no success.
- Second, after data import I would like to retrieve all
information on a probe level for several probe sets. I do
this using the pm()-function, for instance
>pm(CelFiles)[1:16, 1:50]. The problem is that I have to find out first where which exact "location" the probe set of interest has. This is not a big problem, but I thought there might be a more elegant solution to this. 

Thanks in advance,
Roel Verhaak
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