Oncoinformatics Lab

Each data set to be analyzed should be given as tab-delimited text files. Data files can be a single file or 2 separated files. The single file contains mapping information of clones and spot intensities. Mapping information and spot intensities can be separated in two files.

Data in a single file

1. file format: tab-delimited text file
2. rows
   • the 1st row; headers
   • from the 2nd row; data
3. columns
   • the 1st column; clone ID (unique id)
   • the 2nd column; chromosome number (1, 2, 3, ..., X, Y)
   • the 3rd column; start positions of clones on the chromosome (relative to the start of the chromosome) (integer)
   • the 4th column; end positions of clones on the chromosome (relative to the start of the chromosome) (integer)
   • the 5th column; block number of array (integer)
   • the 6th column; column position of spot in a block (integer)
   • the 7th column; row position of spot in a block (integer)
   • the 8th column; red channel foreground intensity
   • the 9th column; red channel background intensity
   • the 10th column; green channel foreground intensity
   • the 11th column; green channel background intensity
   • the 12th column; flag
4. example
   

Data in 2 separated files

• the file containing mapping information
  1. file format: tab-delimited text file
  2. rows
     • the 1st row; headers
     • from the 2nd row; data
  3. columns
     • the 1st column: clone ID (unique ID)
     • the 2nd column: chromosome number (1, 2, 3, ..., X, Y)
     • the 3rd column: start position of the clone in chromosome (integer)
     • the 4th column: end position of the clone in chromosome (integer)
  4. example
     
• the file containing spot intensities
  1. file format: tab-delimited text file
  2. rows
     • the 1st row; headers
     • from the 2nd row; data
  3. columns
     • the 1st column; clone ID (unique id)
     • the 2nd column; block number of array (integer)
     • the 3rd column; column position of spot in a block (integer)
     • the 4th column; row position of spot in a block (integer)
     • the 5th column; red channel foreground intensity
     • the 6th column; red channel background intensity
     • the 7th column; green channel foreground intensity
     • the 8th column; green channel background intensity
     • the 9th column; flag
  4. example