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Panuwat Trairatphisan edited this page Jul 9, 2019 · 4 revisions

Frequently Asked Questions (FAQs)

Input format of nodes' name in CARNIVAL and LP file writing

After providing the input files to the CARNIVAL pipeline, the network descriptions and information of measurements will be extracted in order to write a linear programming (LP) file which can be read and solved by the interactive version of CPLEX. The description of the LP file has to be in a highly standardised format and certain characters, when present, might interfere with correct reading of the LP files. The following symbols are therefore not allowed to be used in the node's name:

  • Algebra Math symbols such as plus '+' or minus '-'
  • Slash '/' and backslash ''
  • Colon ':'
  • Comma ','
  • Bracket '[]' and curly bracket '{}'
  • Empty space " "

The safest symbol to replace these prohibited symbols is either an underscore '_' or a semi-colon ';'. Please note that some gene symbols e.g. "HLA-DQB1-AS1: HLA-DQB1 antisense RNA 1" contains the negative/hyphen symbol. Therefore, please consider revising the network input file (PKN) with gene symbols before proceeding.

No solution was obtained after the optimisation

There are multiple causes which might lead to no resulting network. Several suggestions are listed as follows:

  • Optimisation time is too short (default timelimit=600 [10 minutes]: to increase)
  • The node penalty (beta) is too high (default betaWeight=0.2: to decrease)
  • There is no path linking between measurements and inputs (to check and revise PKN)
  • A full file path was assigned as the result folder name in the runCARNIVAL function (Result_dir: to change into relative path e.g. "output/Results_CARNIVAL"), see Issue #10
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