Using batch creator script

This is a tutorial for the Batch Creator Script which makes annotating and creating batch files for microarray data much faster.

How the script works

You have 3 files total. One is called a template, one the data file, and the final is the completed batch file.

Template file

The template file contains only 2 rows. The first is the headings for each column (from "Result_Set_Name" to "PROBE_SET_ALGORITHM"). The second row will contain any "template" information. The second row should have data in any column that includes information that will never change for that template type. If you have multiple array types that you are loading you can make different templates.

• An example of this is the "Experimenter" column.
  • The name of the experimenter will be the same for every row in the final batch column. You only need to write the name of the experimenter in second row even if the final batch file will contain more than 2 rows.

Rows included in my template for ASv2 arrays:

Coulmn D: Print Name

Affymetrix Ecoli_ASv2

Column H: Exp File Location

affy2_generic.EXP

Column K: SINGLE SCAN FILE LOCATION

noimage.DAT

Column N: Normalization Type

Computed

Column P: Experimenter

DSIEGELE

Column T: Individual User

DSIEGELE

Column U: PROBE_SET_ALGORITHM

Affymetrix MAS 5

Data File

The data file will contain any information that changes from batch file to batch file. This file will contain the as many rows as needed, but the first row will always contain the headings (Result_Set_Name" to "PROBE_SET_ALGORITHM").

Where to find the script

Tetramer: ul/SMD/Batchcreator/