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?

Regards,
Ingrid



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Ingrid H.G. Østensen
Bioinformatics user support (NMC)
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center
0310 Oslo

E -mail: ingrid@microarray.no
Phone:  +47 22 93 54 11
Fax:  +47 22 52 24 21



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