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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).

LOH File Format

This is a tab-delimited file format that contains the output results of the LOH module. The LOH module, a SNP analysis module, detects loss of heterozigosity (LOH). The LOH file format is organized as follows:

  1. The first line contains a list of labels identifying the paired samples.
    • Line format:
      SNP (tab) Chromosome (tab) PhysicalPosition (tab) (pair_1_name) (tab) ... (pair_N_name)
    • For example:
      SNP (tab) Chromosome (tab) PhysicalPosition (tab) SM-12VZ (tab) SM-12W1
  2. The rest of the SNP file contains one row of data for each probe.
    • Line format:
      (snp) (tab) (chromosome) (tab) (position) (tab) (pair_1_loh) (tab) ... (pair_N_loh)
    • For example:
      SNP_A-1855068 (tab) 17 (tab) 41089766 (tab) R (tab) R
    LOH call values are:
    • L (LOH): AB in normal and A or B in tumor
    • R (Retention): AB in both normal and tumor or No Call in normal and AB in tumor
    • C (Conflict): A or B in normal and AB in tumor
    • N (Non-informative call): A or B in normal, or No Call in normal or tumor

Sample LOH file: mynah.loh

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Updated on May 02, 2013 14:43