Once you have the CFG names for your glycans, we must now arrange the microarray data in a format which is recognizable by the GLAD tool. The GLAD tool utilizes tab-delimited text files as its input. The essential format of the file must contain the following headers:
- ID: Numbers only e.g. 1,2,3,4 … Preferably start from 1.
- Name:
- Put the Glycan Names in CFG format here. For alpha or beta use a or b for e.g. “Gala1-3” means Galactose-alpha-1-3.
The GLAD tool uses the “Name” field to generate the structure of the glycan. Therefore it is critical to have the correct name format here. - If specific glycans are not known for the spots, for example in the case of “shotgun” arrays, use names which are composed of alpha-numeric characters (A-Z+a-z+0-9) along with spaces, hyphens and underscores. Keep the name as descriptive as you like, as you can filter data based on the name field.
- Put the Glycan Names in CFG format here. For alpha or beta use a or b for e.g. “Gala1-3” means Galactose-alpha-1-3.
- RFU: The Relative Fluorescence Units is the signal intensity data for the array results
- SD: The standard deviation for the RFU results
- CV: The coefficient of variance for the results which can be calculated as the (SD/RFU)*100
- Rank: The rank for the results. You can use the =RANK.EQ() or the =RANK.AVG() functions in Excel to calculate the Ranks within the dataset.
- Name2: Alternative names for the glycan on the microarray. Follow rules like Name.
To enable easier comparisons between data which are run on similar arrays, try to keep the ID, Name and Name2 in the same order for all your files.
Example Data File Structure
| ID | Name | RFU | SD | CV | Rank | Name2 |
| 1 | Glcb1-4Glcb1-4Glc-AEAB | 321 | 5 | 1 | 3 | Cellotriose DP3 |
| 2 | Glcb1-4Glcb-4Glcb1-4Glc-AEAB | 2870 | 30 | 11 | 2 | Cellotetraose DP4 |
| 3 | Glcb1-4Glcb1-4Glcb1-4Glcb1-4Glc-AEAB | 4400 | 23 | 5 | 1 | Cellopentaose DP5 |
| 4 | Glca1-4Glca1-4Glc-AEAB | 7 | 4 | 53 | 4 | Maltotriose DP3 |
| 5 | Glca1-4Glca1-4Glca1-4Glc-AEAB | 5 | 3 | 63 | 5 | Maltotetraose DP4 |
Sample Excel Workbook
Click Here to download a sample Excel Workbook with the CFG data in the GLAD format.
Saving the File
The GLAD toolkit reads in your data as a tab-delimited text file. It is therefore important that you save your data in excel as a tab-delimited .txt file.
Using a descriptive name which describes the sample usually helps in loading the data into GLAD and having descriptive Data Name will allow you to use the filter function better.
Additionally avoid spaces in the file name. This can create some issues in filtering data if you choose to use the file names as the Data Titles.