Parameters file name has to be
annotation.params name is also supported as a legacy.
Attention: The data file referred by
ANNOTATIONS_FILE field of the
mrna_annotation.params file is expected to have a header (first line is skipped). While the data file referred from
annotation.params must not have a header. Such distinction made for backward compatibility reasons: old platform files did not have a header.
The annotation data file has to have following columns:
|GPL_ID||Platform id (e.g.
|PROBE_NAME||Probe name (e.g.
|GENES||Gene name (e.g.
|ENTREZ_IDS||Entrez gene id (e.g.
|ORGANISM||Species name (e.g.
This is the data file format:
The first row must contain
ID_REF as the first column, which will be the probe name in the respective platform. These must match the probe names when the platform was loaded. The order is not important, but the set of probes in the data file must match exactly the set of probes for the platform.
The subsequent rows are the sample names, whose set must match that of those in the
SAMPLE_CD column in the mapping file. Again, the order is not important.
Empty cells are not allowed. Zeros, negative values and NaNs (input as U+FFFD) are allowed and have the same effect among each other (see below).