It is extremely important to correctly specify the experiment treatment. The treatment consists of one or more factors (e.g. species, innoculated/mock innoculated, tissue type), each of which will have two or more levels. For example, see BB1 ('Cross-species Detection in Barley1 GeneChip Array') in which the factor is species which has 6 levels, Barley, Wheat, Oat, Sorghum, Corn, and Rice.

An example of a more complex treatment is VV2 ('Long-term Salt & Water Stress in Grapes') in which the factors are time, with 5 levels of different time points and stress, with 3 different types, or levels of stress.

And finally, a fairly complex treatment can be seen in BB4 ('Mla-specified Transcriptional Responses in Barley-Powdery Mildew Interactions'). There are 3 factors in this experiment, genotype, pathogen isolates, and time. There are 3 different genotypes, 2 pathogen isolates, and 6 time points.

Because it is so important to specify the treatment correctly, you may wish to consult with the plexdb data curator before beginning to submit your experiment.

After you have defined your factors and levels, you will be asked to indicate how many replicates you did for each treatment.

1. When you first enter the treatment page you will see this box:
   
   Select your 1st factor from the drop-down list and enter the number of levels.
   
   If your experiment has more than one factor, click the 'Add a new factor' to get a new factor row.
   
   
   
   
2. After setting your experiment factors, click the 'Set Factors' button to get a table of all your factors and levels.
   
   
   
   
3. Fill in all of the factor names and make any other adjustments that may be necessary, such as changing the order of the factors using the up and down arrow on the left side of the factor box.
   
   
   
   
4. When you have finished setting the factors and levels, click the 'Save and Set Replications' button to continue.
   
   NOTE: take some care with setting the treatment factors and levels correctly the first time since you may lose some of your work if you have to return and make changes.
   
   
5. On the next page you will be asked to fill in the number of replications of each treatment.