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