problem with Pbase mapping vignette
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nic.bowman • 0
@nicbowman-8599
Last seen 7.1 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  Perhaps I am accessing an outdated version?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 • 800 views
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@sebastian-gibb-6858
Last seen 4.0 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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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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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 Next there is a line Created in the output with an outdated date: Created : Wed Jul 16 02:58:33 2014.