[BioC] Normalization question

[Yong Li]

Dear list,

I have finished analyzing an Arabidopsis ATH1 dataset. The data consists 
of 3 mutants and one wild-type from a tissue. I have used affy, limma 
and gostats and things worked out fine. Now the biologist who provide 
the data would like to compare our wild-type data to some other public 
available Arabidopsis array data from two other tissues from wild-type 
to find DEG. I have searched in GEO and indeed found some datasets (also 
Affymetrix ATH1) and the CEL files are available. They also belong to 
datasets consist of mutant and wild-type, or treatment and untreated 
controls. My questions are:

1) Is it ok to just include the wild-type subset from a GEO dataset for 
my further analysis?

2) Which normalization is suitable in this case to make them comparable 
to our data? For our own data I used RMA.

Thanks in advance for any suggestions.

Best regards,
Yong