Sample MetaData File

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ArrayLand

SampleMetaDataFile.png

A tabular file that contains metadata information for one or more samples. Usually required for generating .alv and .tlv files for publishing to ArrayLand.

An example Sample MetaData File can be found here

Row names: sample IDs where valid characters are A-Z a-z 0-9 - _ # . / and space

Column names: Sample MetaData column names where ( ) will be replaced with [ ] and \ ' , ; " will be replaced with _. Note, it is also best to avoid the following characters as they are not acceptable when building statistical model statements both in Array Studio and other tools like R and SAS: ~ + - * / : ^ | Similarly, avoid starting a name with a digit. Use the ToolTipText and Alias Column Properties to supplement a coded column name.

  • Any names listed in Comparison MetaData File MetaColumns must also be a column in the Sample MetaData File.
  • Treatment, CellType, and Tissue are required MetaColumns in the Comparison MetaData File,
    so must also be included in the Sample MetaData File.

Warning.png WARNING:
The columns DiseaseCategory and TissueCategory are automatically generated from DiseaseState and Tissue, respectively; these columns cannot be manually specified


DiseaseCategoryVocabulary.png TissueCategoryVocabulary.png

The image below shows an example of a metadata table before registry in the land.

InputDiseaseLandMetadata.png

DiseaseCategory and TissueCategory were auto-filled. They were not provided manually in the input table above. AutogeneratedDiseaselandmetadata.png


Hierarchical Display

To display metadata variables in a tree structure when browsing data in the Land, specify the structure in column names like:

ID SubjectID ProjectName Demography[DM]\SEX Demography[DM]\AGE Exposure[EX]\Treatment[EXTRT]
Sample1 Subject1 StudyA M 65 CMPD001
Sample2 Subject2 StudyA F 32 PLACEBO
Sample3 Subject1 StudyB F 56 CMPD005

So the variables appear as     HierarchicalSampleMeta.png

Warning.png WARNING: When loading new metadata, the structure as specified in the most recent file will overwrite any existing structure.


GeneticsLand

ProjectName is required due to the project level access controls - if a sample is not associated with a project, it will be hidden from all non-admin users.


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