Differential gene expression and corelation analysis RPPA data

Question

[prawat2009]

Hi, I am a newbie in bioinformatics and learning to analyse RPPA data. I have normalised data from the sequencing center with Normlinear values given in excel files. Each file has a control and two replicates. And I have 3 datasets per sample. I want to do differential gene expression analysis from this data. Can anybody help me in guiding which pckages can I use in R. I tried using limma but not sure if it would be good for RPPA data.

Thanks

[h.mon]

I suppose RPPA is Reverse Phase Protein Array, correct?

[prawat2009]

Yes, you are correct..