Hi, 

I am using the R package SimpleAffy, now I have a conceptual question regarding the scale factor. Seems that Affymetrix recommend the scale factor should be within 3 fold, the way I understand the scale factor is that it is the ratio between the trimmed mean of one chip (normalized by MAS5) to the target value (say, 100 or 500). According to the manual for QC in SimpleAffy: 

"Large variations in scale factors signal cases where the normalisation assumptions are likely to fail due to issues with sample quality or amount of starting material."

I am getting a little confused about EXACTLY what does scale factor mean:
A. The ratio between the trimmed mean of each chip to a target value
B. The ratio between the trimmed mean of each chip to the trimmed mean of all the chips. 

because the above section seems to me that as long as there is small variation in the scale factor, the quality is no problem. What about all the arrays have scale factor in the range (10.1-10.2)? The scale factor has almost no variation, but they are much higher than 3. or I am misunderstanding some part? 


Thanks a lot!

James

       
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