[BioC] Compare results from different analysis (Affymetrix)

James W. MacDonald jmacdon at med.umich.edu
Mon Dec 11 15:54:36 CET 2006

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?

Doing everything separate like that is a very bad idea. You will not be 
able to tell if differential expression is due to biological differences 
or because you ran the analysis separately.

Instead, you should try either justRMA(), which is more memory efficient 
and may be able to process all the chips at once, or RMAexpress, which 
is a standalone executable that can run lots of chips with not much 
memory. You can find RMAexpress here:




> Regards, Ingrid
> --- Ingrid H.G. Østensen Bioinformatics user support (NMC) Department
> of Tumor Biology (Montebello) Rikshospitalet-Radiumhospitalet Medical
> Center 0310 Oslo
> E -mail: ingrid at microarray.no Phone:  +47 22 93 54 11 Fax:  +47 22 52
> 24 21
> [[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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