Dear list,

I would like to apply the Rank Products method in a two-color experiment on
breast cancer data in order to identify differentially expressed genes
between ER+ and ER- samples. I downloaded the R-package RankProd and tried
to use the RP function. The experiments were done with a common reference
for all the samples examined. So the sample of interest was at the one
channel and the reference on the other. I was wondering in the RP function:

RP(data,cl,num.perm=100,logged=TRUE,na.rm=FALSE,gene.names=NULL,plot=FALSE,
rand=NULL),

where cl is said to be:
cl:  a vector containing the class labels of the samples. In the two class
unpaired case, the label of a sample is either 0 (e.g., control group) or 1
(e.g., case group). For one class data, the label for each sample should be
1.

Can I use 1 for ER- and 0 for ER+ samples from the matrix that I have? My
matrix contains gene expressions as rows and samples as columns. The columns
are only the samples of interest (ER+, ER-), not the reference. I am a bit
confused with the exact meaning of "control group" and "case group".

Thanks a lot!
Eleni

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