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AgilentMicroarray (.txt)

  • Import fully supports the Agilent microarray format.

Background & Context

    • Agilent microarray data format.
    • File format used for the storage and exchange of microarray data and metainformation.
    • ASCII format.
    • Output format of Agilent Feature Extraction and Agilent Genomic Workbench (AGW) software.
    • Contains three subtables, storing the Feature Extraction parameters, microarray-level statistics and feature-level data.

Import

  • Import["file","AgilentMicroarray"] imports data from any Agilent microarray file.
  • Import["file",{"AgilentMicroarray",elem}] imports the specified element.
  • Import["file",{"AgilentMicroarray",{elem1,elem2,…}}] imports multiple elements.
  • Import["file",{"AgilentMicroarray",elem,subelem}] imports the specified subelement.
  • Import["file",{"AgilentMicroarray",elem,{subelem1,subelem2,…}}] imports multiple subelements.
  • See the following reference pages for full general information:
  • Importimport from a file
    CloudImportimport from a cloud object
    ImportStringimport from a string
    ImportByteArrayimport from a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Common data representation element:
  • "FeatureTable"raw feature table
    "LabeledFeatureTable"feature table as a list of rules
  • Meta-information element:
  • "Header"Feature Extraction parameters given as a list of rules
  • Array-wide statistics element:
  • "Statistics"array-wide statistics given as a list of rules
  • Use Import["file",{"AgilentMicroarray",elem,"Elements"}] to list the subelements available in each of the three main tables ("LabeledFeatureTable", "Header", "Statistics").
  • Import uses the "FeatureTable" element by default.

Examples

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Basic Examples  (2)

Import array-wide statistics:

Wolfram Language code: Import["ExampleData/GSM263810.txt", {"AgilentMicroarray", "Statistics"}] //Short[#, 5]&

Import parameters used in the Feature Extraction software:

Wolfram Language code: Import["ExampleData/GSM263810.txt", {"AgilentMicroarray", "Header"}] //Short[#, 5]&

List the data available for each feature:

Wolfram Language code: Import["ExampleData/GSM263810.txt", {"AgilentMicroarray", "LabeledFeatureTable", "Elements"}]//Short[#, 10]&

Import the gene names and log ratio for several features:

Wolfram Language code: Import["ExampleData/GSM263810.txt", {"AgilentMicroarray", "LabeledFeatureTable", {"GeneName", "LogRatio"}, Range[50, 60]}]//TableForm@Transpose@#&

Scope  (1)

Create a digital rendering of a microarray based on the fold changes of the probes:

Wolfram Language code: data = Transpose@Import["ExampleData/GSM263810.txt", {"AgilentMicroarray", "LabeledFeatureTable", {"PositionX", "PositionY", "LogRatio"}}]; data[[All, 3]] = Rescale[data[[All, 3]]]; RG[z_] := Blend[{Green, Black, Red}, z] Graphics[Table[{RG[i[[3]]], Disk[i[[1 ;; 2]], 5]}, {i, data}], ImageSize -> 500, Background -> Black]