List of System Messages

Initialization Messages

'Warning: GeneLinker™ has failed to initialize correctly - Perhaps there is another instance already running.'

One common reason for this is that you may have clicked too many times and started more than one instance of GeneLinker™. After this message is displayed GeneLinker™ exits. To fix this problem, ensure GeneLinker™ is not already running, then restart the application.

'Warning: GeneLinker™ will expire on: Expiry Date.'

'Preference file missing a ppsi.genelinker.license.filename entry. GeneLinker™ cannot start.'

'Could not find license manager file. GeneLinker™ cannot start.'

'License for GeneLinker™ has expired. GeneLinker™ cannot start.'

'Couldn't get license for GeneLinker™. GeneLinker™ cannot start.'

Ensure the files listed as ‘missing’ or ‘not found’ are present in the license folder in the GeneLinker™ directory, or obtain a new license if required, then restart the application. Alternatively, call Technical Support.

Messages on Startup

'Thank you for evaluating GeneLinker. Its free demonstration period has expired. To purchase a license, contact sales at Predictive Patterns Software Inc..'

'The GeneLinker license for this computer has expired. To renew your license, please contact sales at Predictive Patterns Software Inc.. If you have an up-to-date GeneLinker license key for this computer, click 'Edit License Information'.

'The GeneLinker license for the license server 'Your Server Name' has expired. To revew your license, please contact sales at Predictive Patterns Software Inc.. If you have an up-to-date license key for this computer, click 'Edit License Information'.

'The GeneLinker license for this computer is invalid. To obtain a license, please contact sales at Predictive Patterns Software Inc.. If you have a GeneLinker license key for this computer, click 'Edit License Information'.

'The GeneLinker license for the license server 'Your Server Name' is invalid. To obtain a license, please contact sales at Predictive Patterns Software Inc.. If you have a GeneLinker license key for this computer, click 'Edit License Information'.

'The GeneLinker license server 'Your Server Name' was not found on your network. If the name or address of your GeneLinker license server has changed, click 'Edit License Information'.

'GeneLinker requires the GeneLinker License Manager Service, but it isn't currently running on this computer. Restarting the computer should restart the service. Failing that, reinstalling GeneLinker may help. If problems persist, contact technical support at Predictive Patterns Software Inc..'

'GeneLinker could not connect to the license server on the network computer 'Your Server Name'. If the name or address of your GeneLinker license server has changed, click 'Edit License Information'.

'The GeneLinkerPlatinum.conf file is missing an entry for the license file name. The application can not start.'

No license file name entry in the configuration file.

'Could not find the license.dat file at the location specified within GeneLinkerPlatinum.conf. The application can not start.'

No license file in specified location.

'Could not connect to the FlexLM license manager. The application can not start.'

The server (lmgrd) has not been started yet, or the wrong port@host or license file is being used, or the port or host name in the license file has been changed.

'GeneLinker Platinum could not obtain license from server. All available licenses are checked out.'

Licensed number of users already reached.

'The feature requested could not be found in the license file for GeneLinker Platinum. The application can not start.'

The feature could not be found in the license file.

'GeneLinker Platinum's license server does not support the feature requested. The feature may have expired or the version number is not supported.'

The feature has expired (on the server), or has not yet started, or the version is greater than the highest supported version.

'GeneLinker Platinum's license server has detected invalid license keys. Please see your system administrator to obtain valid license keys.'

The code in the license file line does not match the other data in the license file.

Messages after Startup

'GeneLinker has lost communication with its licence manager service running on the network computer '<server name>'. GeneLinker is now trying to re-establish contact, but will automatically shut itself down if it fails to do so before <current time + 10 minutes>. Any experiments in progress at that time will run to completion and will be saved automatically before GeneLinker quits.'

Three possible reasons. Connectivity problems (physical), the server has crashed, or the license manager is not running.

'Connection has been re-established with the license manager. GeneLinker will not shut itself down.'

The problem that caused the lost communication with the license manager has been resolved within the time out period (10 minutes).

'There has been no connection to License Manager for the past 10 minutes. Application is being shut down.'

All attempts to reconnect to the license manager have failed during the last 10 minutes.

License Messages

'A problem was encountered while initializing the dialogue needed to update your license file. The application will exit after this dialog is closed. Please check the log files for the problem details.'

'The licensing information for GeneLinker has been updated. You must restart this computer for these changes to take affect.'

'The server name for this GeneLinker floating client has been updated. You must restart GeneLinker for this change to take affect.'

Upgrade Messages

'Welcome to GeneLinker! GeneLinker is upgrading your data repository to the latest format.'

'This should take less than a minute or two.'

'This may take a few minutes.'

Data Import Messages

'Could not open <filename> for reading.'

This means that the file <filename> is either not present on the system or the user does not have permission to read it.

'Could not open <filename> for writing.'

This means that the user does not have permission to open the file <filename>, which will generally be a temporary output file opened by a script.

'Could not find header in file: <filename>.'

This means the file is corrupt or has the wrong format, and the script cannot detect the data header.

'Could not find data in file: <filename>.'

This means the file is corrupt or has the wrong format, and the script could not detect the start of the numeric data in the file.

'Could not understand expression column: <column name>.'

This means the script could not find a column of the given name in the file. The header is probably corrupt, or the file is of the wrong format.

'Could not understand confidence column: <column name>.'

This means the script could not find a column of the given name in the file. The header is probably corrupt or the file is of the wrong format.

'Script did not get any input files!'

The script has been run without any input files selected.

'Script did not get any expression output file!'

The script was not passed a temporary filename for the preprocessed results.

'Incorrect file format.'

The GenePix header string (ATF) was not detected in a GenePix Axon Text File.

'The name 'dataset' is already taken. Enter a unique name for this dataset.'

Variable Import Messages

'A variable named 'variable name' already exists. To create a new variable type, you must use another name.'

'A variable named 'variable' already exists in this dataset. To import a new variable, you must use another name.'

Navigator Messages

'Are you sure you want to delete 'your experiment' experiment? This action cannot be undone.'

'Are you sure you want to delete 'your experiment' and all of its derived experiments? This action cannot be undone.'

'Are you sure you want to delete these experiments? This action cannot be undone.'

'Are you sure you want to delete these experiments and all of their derived experiments? This action cannot be undone.'

Filtering Messages

For N Fold Culling With N:

'The user specified value can not be less than or equal to zero.'

For N Fold Culling With Number of Genes, Range Culling, Maximum Culling, Spotted Array N Fold Culling:

'The user specified value can not be less than or equal to zero.'

'The user specified value cannot be larger than or equal to the number of genes.'

Normalization Messages

'The Gene List just created cannot be used in this experiment. You have selected 'one gene (for example). Please see the Help topics on using gene lists in Normalization. This new Gene List will still be available for other experiments.'

'The Gene List just created cannot be used in this experiment. You have selected all the genes. Please see the Help topics on using gene lists in Normalization. This new Gene List will still be available for other experiments.'

Clustering Messages

For K Means For the Number of Means:

'The number of clusters must not be less than 2.'

'The number of clusters must not exceed the number of clusterable items: #.'

For Jarvis-Patrick for the Neighbors to Examine:

'The number of Neighbors to Examine must not be less than 2.'

'The number of Neighbors to Examine must not exceed the number of clusterable items: #.'

For the Neighbors in Common:

'The required number of Neighbors in Common must not be less than 1.'

'The required number of Neighbors in Common must not be greater than or equal to the number of Neighbors to Examine.'

Make the required changes to the clustering parameter Gold(s) and try again. If that is unsuccessful, call Technical Support.

Message when Launching Summary Statistics

'Summary Statistics requires a selection that contains at least two data values. Change your selection and try again.'

Select a dataset or gene/sample with more than one value to view summary statistics.

Messages when Exporting Images

'Error encoding PNG file: <filename>'

'Ran out of memory making PNG file: <filename>'

'Error writing out file: <filename>'

If any other applications are running, close them to free up some memory. Try the export operation again. If that is unsuccessful, exit GeneLinker™, restart the application (and possibly reboot the computer), and try the export again. If that fails, call Technical Support.

Experiment Messages

'The experiment couldn't be completed. Check that the operation and its parameters are appropriate to the data.'

The most common cause of this message is GeneLinker™ attempting to carry out an impossible mathematical operation, such as dividing by zero or taking the logarithm of a negative number.
Create a table view of your data and inspect it for negative numbers, genes with zero expression or other features that might invalidate the operation you requested. Once you have determined the source of the problem, try filtering or preprocessing the data then run the operation that previously failed.

'Are you sure you want to cancel the experiment?'

Gene Lists Messages

'Are you sure you want to delete gene list 'Your Gene List'? This action cannot be undone.'

'Are you sure you want to delete these 'Your Gene Lists' gene lists? This action cannot be undone.'

Create Classifier Messages

'The number of learners must be between 2 and the number of samples in the dataset (inclusive).'

'The number of hidden units must be between 1 and four times the number of genes in the dataset (inclusive). In general, the number of hidden units should be much smaller than the number of genes.'

'The number of conjugate gradient steps must be between 2 and 2147483647 (inclusive). In general, the number of steps should be much less than 1,000.'

'The maximum number of iterations must be between 1 and 2147483647 (inclusive). In general, the maximum number of iterations should be less than 10,000.'

SLAM Messages

'This value must be at least zero.'

'The number of iterations must be greater than zero.'

'The range for Matthews numbers is -1 through 1, inclusive. In general, associations with Matthews numbers that are less than 0.5 or so are not of interest.'

'The minimum support measure must be between one and the number of samples (inclusive).'