Hi!
I am confused with some terms, so, I appreciate any help in advance.
Array data sets are usually reported as intensity levels of probes (expression values). Some researchers report their data in preprocessed forms (RMA, MAS5, etc.); however, I came across some preprocessed samples on NCBI GEO termed as "RMA log2 intensity". I got confused, since seemingly that experiment was done in single color arrays, so, log2 is a bit confusing. Isn't log2 fold-change for double-color arrays? Or simply "RMA log2 intensity" means that they calculated log2 of intensity levels and performed RMA normalization on the data. If this is the case, log2 does not necessarily denotes fold-change (am I right?). Furthermore, what is the necessity of log2 for intensity values in single-arrays?
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