I have a problem in dealing with a classic breast cancer dataset from the following paper.
I downloaded data from here. But when I do the visualization of probe signal, it seems that data has not been normalized and they usually appear around zero which is on the contrary to normal data with mean around 7 (after log2 transformation). I have noticed that this array chip is not standard one and the authors developed by themselves. So I wonder what kind of data processing method should be performed to make the analysis meaningful.
BTW, where could I obtain some documentation for this array data expect read me files accompanied with array matrix from download site. For example, I met a problem in understanding the header of the array data.
"Substance Gene Log Ratio Log Ratio Error p-Value Intensity Flag"
I am not quite sure if it is OK to adopt Log Ration as the signal value, while as for Log Ratio Error p-Value and Intensity, what do they mean?
Thanks a lot and I am looking forward your reply.