[BioC] Compare results from different analysis (Affymetrix)

[Sean Davis]

On Monday 11 December 2006 09:33, Ingrid H. G. Østensen wrote:
> Hi
>
> I am currently working on data from the Affymetrix platform. I have gotten
> 36 arrays that are divided into 3 groups: 3 different cell lines where two
> are derived/changed versions of the first. These 3 groups are divided into
> 4 time points: 0 (control), and 3, 24 and 72 hours. There are 7 comparisons
> that are to be done: One for each group (3) and one for each time point
> (4).
>
> Because this is the Human Genome U133 Plus 2 Array from Affymetrix I can
> not read all the files into R/Bioconductor at once, I run out of memory. I
> can divide the files into the different comparisons groups and work on
> these but it is one thing that troubles me. If I do the seven different
> comparisons (everything separate: loading the data, normalization, analysis
> etc) can I compare the different results? For example: Lock at time point
> 24 and 72 to find the differences between them, or cell group 1 and 2?

Hi, Ingrid.  You might start by letting us know how you are trying to load the 
arrays into Bioconductor.  There may be a way to load all of them (by using 
justRMA instead of RMA, for example).  Include the output of sessionInfo() so 
that we know the OS and R version, as well as the amount of RAM in your 
machine.  If you can load all the arrays simultaneously, it may make your 
life easier down the road.

Sean