ExpressionData:ReporterIDs
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[edit] Terminology
In VectorBase we tend to refer to the biological sequence spotted on your arrays as reporters although we may also use the word probe. The reporter ID may be refered to differently by your array software (some software uses "Gene ID", please see the next section).
[edit] No gene names please
It is strongly recommended that the reporter ID column in all your files (array design and data files) contains arbitrary names or numbers rather than gene names or ids. The reason for this is that if you design a reporter against a certain gene, you may find that the sequence does not uniquely map to that gene (or may not map at all) in future genome assemblies and gene builds. Reporters named after genes are therefore potentially misleading.
If you are designing a new array, recommended reporter ID naming schemes are:
- short prefix identifying your lab, species and array version followed by the reporter serial number, e.g. SmithAgamV1000001
- clone name
- LIMS well location (with a prefix perhaps)
[edit] Uniqueness of reporter IDs
At present we are unable to accept your array design if identical reporter IDs are used for different reporters on another array design (for any VectorBase species). Therefore if you are designing a new array it would be advisable to create reporter IDs which contain the initials of your lab or institution.
[edit] Special characters
Please avoid underscores and colons if possible.
[edit] Result files
Of course, we also ask that the reporter IDs in the array design file match those in the raw data files.
