I did misunderstand your intention. However I still do not understand your solution. If I assume that the zero data is really a small positive number that displays as '0.00', its log should be a negative number whose magnatude exceeds any of the other logs. (e.g. log(0.001) = -6.9) Setting the log to zero assumes that the raw value is e (2.71...). Note: All other values are between .001 (log(.01) = -4.6) and .99 (log(.99) = -.01).
Re^4: Calculate log of matrix values
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What a difference a day makes. Of course it is an excelent idea to replace the zero in the raw data with a small number (Especially if there is reason to believe that the zero is the result of truncation.)