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Module detail: MIAMExpress.pm |
ArrayExpress::Curator::MIAMExpress - a module used by expt_check.pl
use ArrayExpress::Curator::MIAMExpress;
my $checker = ArrayExpress::Curator::MIAMExpress->new({
mx_login => $login,
mx_title => $title,
});
$checker->check();
This module provides a set of subroutines used by the experiment checker script to interact with a local MIAMExpress installation. It optionally exports just two (fairly heavyweight) subroutines. Please see the end of this document for the tests carried out by this module.
The following options must be used in addition to those provided by the parent class (see the ArrayExpress::Curator::ExperimentChecker manpage):
mx_loginThe submitter login name associated with a MIAMExpress
submission. See mx_title.
mx_titleThe title of a MIAMExpress submission. See mx_login.
The following tests are performed by this module, with output printed to the error and/or report filehandles (see the ArrayExpress::Curator::ExperimentChecker manpage for a list of more general tests which are also run):
Checks the linking between sample, extract, labeled extract and hybridization, and writes a biomaterials log file which attempts to portray these links in ASCII. Highlights BioMaterials which have not been properly linked through to hybridizations (biomaterials log).
Generates a report showing how hybridizations have been linked to experimental factor values, and vice versa (biomaterials log).
Generates a report on all the annotation attached to the samples in the experiment (sample log).
Checks whether the publication details include standard Pubmed abbreviations; also alerts the curator if a new publication (``other'') has been indicated (error log).
Alerts the curator if QVS entries have been used under Experiment or Sample annotation (error log).
Alerts the curator if ``Other'' entries have been used under Experiment, Protocol or Sample annotation (error log).
Alerts the curator if a final data matrix file has been supplied without a transformation protocol (error log).
Alerts the curator if protocols with fewer than 50 characters are submitted (error log).
Alerts the curator if a pooling protocol has been linked to a submission (error log).
Alerts the curator if normalized data files have been supplied without a normalization protocol (error log).
Alerts the curator if protocols other than pooling, normalization or transformation have not been bound to their appropriate objects (error log).
Prints a table indicating which kinds of raw and normalized data file have been submitted for each hybridization (report log).
Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2005.
Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.