Contrast Type

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This page explains the content of the column '''ContrastType''' in the Excel file, which works as a mapping file in the second step of [http://www.arrayserver.com/wiki/index.php?title=Build_ComparisonLand_From_Raw_Data#Step_2:_Convert_.osprj_file_to_.tlv_files| Build ComparisonLand From Raw Data]
 
This page explains the content of the column '''ContrastType''' in the Excel file, which works as a mapping file in the second step of [http://www.arrayserver.com/wiki/index.php?title=Build_ComparisonLand_From_Raw_Data#Step_2:_Convert_.osprj_file_to_.tlv_files| Build ComparisonLand From Raw Data]
  
So the content in this column must be one of them in the column of '''Recognized term''' in the following table, which are recognized by our land tools.  
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See [[Comparison Categories]] for definitions of the terms, as used by the Land curation team.
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The content in this column must be one of them in the column of '''Recognized term''' in the following table, which are recognized by our land tools.  
  
 
The content of the '''ContrastType''' will be stored in [[TLV]] file, and when these TLV files get published to the land, they will show these content as '''ComparisonCategory''' corresponding to the second column here:   
 
The content of the '''ContrastType''' will be stored in [[TLV]] file, and when these TLV files get published to the land, they will show these content as '''ComparisonCategory''' corresponding to the second column here:   

Latest revision as of 21:58, 12 May 2020

This page explains the content of the column ContrastType in the Excel file, which works as a mapping file in the second step of Build ComparisonLand From Raw Data

See Comparison Categories for definitions of the terms, as used by the Land curation team.

The content in this column must be one of them in the column of Recognized term in the following table, which are recognized by our land tools.

The content of the ContrastType will be stored in TLV file, and when these TLV files get published to the land, they will show these content as ComparisonCategory corresponding to the second column here:

Recognized term ComparisonCategory displayed in land
Disease vs. Normal Disease vs. Normal
Disease1 vs. Disease2 Disease1 vs. Disease2
CellType1 vs. CellType2 CellType1 vs. CellType2
Treatment vs. Control Treatment vs. Control
Treatment1 vs. Treatment2 Treatment1 vs. Treatment2
Responder vs. Non-Responder Responder vs. Non-Responder
Tissue1 vs. Tissue2 Tissue1 vs. Tissue2
Healthy vs. Control Healthy vs. Control
Resistant vs. Sensitive Resistant vs. Sensitive
Genotype vs. Wild Type Other Comparisons
Genotype1 vs. Genotype2 Other Comparisons
Phenotype1 vs. Phenotype2 Other Comparisons
Disease Stage1 vs. Stage2 Other Comparisons
Dosage1 vs. Dosage2 Other Comparisons
Strain1 vs. Strain2 Other Comparisons
Other Other Comparisons
Tips.pngThe controlled vocabulary for ContrastType (the first column in the table above) is case sensitive


Warning.png WARNING: When user specify certain ContrastType in the ContrastMapping.txt file, there might be some limitations for the corresponding column in the design table (the Sample sheet in the Excel file used in step 1 for Build ComparisonLand From Raw Data), which means that certain ContrastType, for instance, if user specify treatment vs. control, it will require some specific column name in the design table including Treatment; SubjectTreatment; TreatmentStatus; Transfection; Infection; SubjectInfection; AllergenChallenge; Stimulation


Here is information to show which column name is required for each ContrastType, so user can follow the principle from the very beginning.

  • "Disease vs. Normal": DiseaseState or OLandDiseaseState or MaternalDisease
  • "CellType1 vs. CellType2": CellType or OLandCellType
  • "Treatment vs. Control": Treatment or SubjectTreatment or TreatmentStatus or Transfection or Infection or SubjectInfection or AllergenChallenge or Stimulation
  • "Responder vs. Non-Responder": Response and (Treatment or SubjectTreatment or TreatmentStatus)
  • "Disease1 vs. Disease2"
  • "Treatment1 vs. Treatment2"
  • "Tissue1 vs. Tissue2"
  • "Healthy vs. Control"
  • "Genotype vs. Wild Type"
  • "Genotype1 vs. Genotype2"
  • "Phenotype1 vs. Phenotype2"
  • "Disease Stage1 vs. Stage2"
  • "Dosage1 vs. Dosage2"
  • "Strain1 vs. Strain2"
  • "Resistant vs. Sensitive"
  • "Other"


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