problem with Pbase mapping vignette
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Entering edit mode
nic.bowman • 0
@nicbowman-8599
Last seen 6.2 years ago
University of Pennsylvania

Hello, 

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  Perhaps I am accessing an outdated version?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:
  [1] A4UGR9 [2] A6H8Y1 ... [8] P04075-2 [9] P60709
Sequence features:
  [1] DB [2] AccessionNumber ... [10] Comment [11] Filename
Peptide features:
  [1] DB [2] AccessionNumber ... [46] spectrumFile [47] databaseFile

 

Specifically, highlighted, you'll see where my data set falls short.  Sequence features should go to [13] and should include "npeps" and "ENST".  Peptide features should only have [28] categories, where you can see my list has 47.

 

thanks for the input!

Pbase • 713 views
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3
Entering edit mode
@sebastian-gibb-6858
Last seen 3.0 years ago
Germany

Indeed it seems you are using an old version of `Pbase`. What does `sessionInfo()` say? Did you try to update `Pbase` using `source("http://bioconductor.org/biocLite.R"); biocLite("Pbase")`?

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Entering edit mode

thanks so much! that solved the problem.

These websites are great for the silly questions to get me over this initial learning hump for working in R.

If you have a second, could you tell me what it was that let you know I was using an old version?

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Entering edit mode

First, I am one of the maintainers and that's why I am knowing that we changed the `p` object in the past sometimes. Next there is a line `Created` in the output with an outdated date: `Created : Wed Jul 16 02:58:33 2014`.

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