[BioC] large amount of slides

[Park, Richard]

Hi Vada, 
I would caution you on doing rma on that many datasets. I have noticed a trend in rma, that things get even more underestimated as the number and variance of the data increases. I have been doing an analysis on immune cell types for about 100 cel files. My computer (windows 2000, 2gb of ram, 2.6 pentium 4) gives out around 70 datasets, I am pretty sure that my problem is that windows 2000 has a maximum allocation of 1gb. 

But if most of your data is pretty related (i.e. same tissues, just a ko vs wt) you should be fine w/ rma. I would caution against using rma on data that is very different. 

hth, 
richard 

-----Original Message-----
From: Vada Wilcox [mailto:v_wilcox at hotmail.com]
Sent: Friday, June 04, 2004 11:06 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] large amount of slides


Dear all,

I have been using RMA succesfully for a while now, but in the past I have 
only used it on a small amount of slides. I would like to do my study on a 
larger scale now, with data (series of experiments) from other researchers 
as well. My questions is the following: if I want to study, let's say 200 
slides, do I have to read them all into R at once (so together I mean, with 
read.affy() in package affy), or is it OK to read them series by series (so 
all wild types and controls of one researcher at a time)?

If it is really necessary to read all of them in at one time how much RAM 
would I need (for let's say 200 CELfiles) and how can I raise the RAM? I now 
it's possible to raise it by using 'max vsize = ...' but I haven't been able 
to do it succesfully for 200 experiments though. Can somebody help me on 
this?

Many thanks in advance,

Vada

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