I am interested in analyzing the data from PRIDE archive (Project PXD000838). This study involves Shotgun Proteomics. My goal is to perform preprocessing of the data and then identify the differentially expressed proteins from it.
I started with the rpx package of R.'pxfiles' usage shows the data has 73 files. Every file (except the readme) is in zipped format. Which of the files should be used for the pre-processing and normalization of the data? What packages should I be using for this purpose? I am very novice in this field. Can anyone please suggest me any way?
Thanks in advance.