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samWieczorek / old_Prostar

Graphical User Interface for the R-package DAPAR
http://www.bioconductor.org/packages/release/bioc/html/Prostar.html
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Questions #2

Closed samWieczorek closed 2 years ago

samWieczorek commented 2 years ago

I have been using Prostar since January, with the last version on my computer being 1.22.4 but I recently downloaded the most recent version and encouter some bugs and difficulties.

  1. How is the MV filtering "Empty lines" in the new version? I don't find the same option for that.
  2. When they ask us to choose an identification (ex. Protein names or gene names), why does it says that I have duplicates in my file?
  3. When they ask us to select Tooltip ID, after i select a few, they don't show up on the volcano plot however...
  4. Same thing When I download the Differential anlaysis table, I used to have all these ID columns too but I only have 1 now.
samWieczorek commented 2 years ago
  1. To reproduce the filter ‘Empty lines’, one must select the following values:
    • Nature of data filter -> « missing »
    • Type of filter operation -> w.r.t the user
    • Scope = « Whole line »
  2. The identification tag must be unique for each peptide/protein. If not, prostar will be unable to decide which peptide/protein to use for some computation if several entities share the same Id. Thus, the message informs you that the colum you have choosen as ‘Identification’ contains the same id in several lines. You juste have to select another column which reflects the id of the entities.
  3. Linked to #4
  4. Linked to #4