I am a graduate student working to re-vamp my lab's proteomic analyses. To start, I am simply working through many of the bioconductor package vignettes. Pbase specifically applies to my goals, but I cannot complete the vignette with the data provided. Perhaps I am accessing an outdated version?
When I first load the p dataset, I am missing some information. I would appreciate being pointed in the right direction or towards the full data set so that I can proceed teaching myself this package!
From my console:
> library("Pbase") > data(p) > p S4 class type : Proteins Class version : 0.1 Created : Wed Jul 16 02:58:33 2014 Number of Proteins: 9 Sequences:  A4UGR9  A6H8Y1 ...  P04075-2  P60709 Sequence features:  DB  AccessionNumber ...  Comment  Filename Peptide features:  DB  AccessionNumber ...  spectrumFile  databaseFile
Specifically, highlighted, you'll see where my data set falls short. Sequence features should go to  and should include "npeps" and "ENST". Peptide features should only have  categories, where you can see my list has 47.
thanks for the input!