Hello, 

I used Bioconductor to statistical process of dual channel microarray using RankProd package.

As user guide suggested, I used that syntax:

> cl=rep(1,4)
> RankProducts(data,cl, logged=TRUE, rand=123)

Because the user guide mentioned the data of dual microarray inputted as log-scaled fold-change (FC) ratio, I prepared the data set of log-scaled FC, but the RankProd just calculated the average FC as (sum of all log-scaled ratio)/4. The log-scale did not considered.

Therefore, my question is:

1. The data set of dual channel microarray must be prepared in decimal number?

2. In fact, i tried to use the transformed data set of dual microarray in decimal number. Because the data set was not log-ratio, i modified the R syntax (logged=TRUE -> logged=FALSE), but it did not work. How should i modify the syntax if i want to the decimal number data set?

Best regards,

Suyeon Kim