Broad TCGA GDAC Blog

Report Guidelines

Here is a quick checklist summarizing the report guidelines:

  • Does the report title follow the guidelines?
  • Does the summary focus on results and does not include any references to figures, tables, or citations?
  • Are all parameters of the pipeline mentioned in the report marked up with “asParameter()”?
  • Are all values of parameters mentioned in the report marked up with “asValue()”?
  • Are all links in the report generated with “asLink()”?
  • Are all filenames mentioned in the report marked up with “asFilename()”, in particular in the “Input” section.
  • Are tables referred to using “asReference( myTable )”?
  • Are figures referred to using “asReference( myFigure )”?
  • Are citations referred to using “asReference( myCitation )”?
  • Do figure and table captions describe the variable names used in column headers and as axis labels?
  • Do figures that potentially might get large (wider than 800 pixels) have a link to the “High-Res” image?
  • Does the report use nomenclature as agreed:
    • miR - Not: microRNA or miRNA
  • Is “writeReport()” being called without “debug=TRUE”?
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