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Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).

GCT File Format

The GCT file format is a tab delimited file format that describes an expression dataset. The main differences between RES and GCT file formats are the RES file format (1) contains labels for each gene's absent (A) versus present (P) calls as generated by Affymetrix's GeneChip software and (2) does not allow missing expression values. Although the GCT file format allows missing values, only a few modules (such as CART, GSEA and HierarchicalClustering) can be run against an expression dataset that is missing values. Most modules do not allow missing expression values.

The GCT file is organized as follows:

  1. The first line contains the version string and is always the same for this file format. Therefore, the first line must be as follows:
    • #1.2
  2. The second line contains numbers indicating the size of the data table that is contained in the remainder of the file. Note that the name and description columns are not included in the number of data columns.
    • Line format:
      (# of data rows) (tab) (# of data columns)
    • For example:
      7129 58
  3. The third line contains a list of identifiers for the samples associated with each of the columns in the remainder of the file.
    • Line format:
      Name (tab) Description (tab) (sample 1 name) (tab) (sample 2 name) (tab) ... (sample N name)
    • For example:
      Name Description DLBC1_1 DLBC2_1 ... DLBC58_0
  4. The remainder of the data file contains data for each of the genes. There is one line for each gene and one column for each of the samples. The first two fields in the line contain name and descriptions for the genes (names and descriptions can contain spaces since fields are separated by tabs). The number of lines should agree with the number of data rows specified on line 2.
    • Line format:
      (gene name) (tab) (gene description) (tab) (col 1 data) (tab) (col 2 data) (tab) ... (col N data)
    • For example:
      AFFX-BioB-5_at AFFX-BioB-5_at (endogenous control) -104 -152 -158 ... -44

Occasionally, GCT files are organized in a transposed structure where the columns represent genes and the rows represent samples. The user should take care to check the organization of the file to ensure that the correct preprocessing is performed on the file. See sample *.gct files that come with the distribution for complete examples of the format.

Sample GCT file: allaml.dataset.gct

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Updated on March 05, 2013 14:37