Using batch creator script: Difference between revisions
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*An example of this is the "Experimenter" column. | *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. | **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. | ||
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Rows included in my template for ASv2 arrays: | Rows included in my template for ASv2 arrays: | ||
Revision as of 19:53, 7 September 2010
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.
| Column | Heading Name | Template Value |
|---|---|---|
| edit table |
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/