Yes, you can add resources to annotate reporters. You will need to upgrade BASE and you may have to contact your system administrator for doing so.

In order to change, remove or add annotation fields attached to reporters, you will need modify the extended-properties.xml file and run a BASE update. Please refer to section Section 21.3, “Installation instructions” for information about both processes. Once done with the upgrade, you'll have to define a new reporter import plug-in. Instructions can be found in Chapter 22, Plug-ins.

The reporter import plug-in can be executed in delete mode. Run the plug-in again and select the same file you just for the import. Select the Mode=delete option. In the Error handling section select the Reporter is used=skip option. This will delete all reporters that was created in the previous import.

BASE requires all reporters (probesets in Affymetrix speak) to be stored in the database before they can be used. The reporter information is typically imported from a reporter annotation file but in some cases the reporter annotation file supplied by Affymetrix fails to describe all reporters (probesets) on a chip. BASE will refuse to store data related to such chips until the missing reporters are added to the database. Hence the rejection of the new root bioassayset.

The resolution is straightforward, simply import the probeset information from the CDF file associated with the array design. The catch is that normal BASE user credential is not enough to perform the import therefore someone with proper credential (the BASE server administrator is one of them) must perform the import. Follow the instructions at Section 10.3.1, “Import/update reporter from files” to import reporters. Make sure to select plug-in option to ignore already existing reporters when starting the import otherwise the existing reporter annotations will be changed. The goal here is to add missing reporters to allow BASE work with your data. The CDF file does not contain any annotation information and cannot be used to annotate reporters.

This requires some work but here is the procedure to remember:

A gal file tells where Reporters have been spotted on an array. So a GAL file can be used to do 2 things

The reporter map and print map importer are used to import features to an array design. The latter one must be used when your array design is connected to PCR plates and supports two file formats: Biorobotics TAM and Molecularware MWBR. See http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php for more information about those file formats. If you are only using commercial platforms or if you do not use plates in the array LIMS, you have no need for the print map importer and should use the reporter map importer instead.

The reporter importer is used to load reporter annotations into BASE.

Try clearing the filter. To do so: use the view / presets dropdown and select the clear filter entry. This will remove all characters in the search boxes and all preselection of item in the drop down lists. If this does not solve your problem, then check if the view / presets has the owned by me entry selected.

Yes, you can display many more columns. See Section 6.4.3, “Configuring which columns to show”.

Of course it is. See Section 6.4.1, “Ordering the list”.

No. This is not possible at the moment. The annotations are always sorted by the name of the annotation type.

Yes, you can. From the sample list select a number of samples by marking their checkboxes. Then click on the Pool button. For more information see Section 17.3.1, “Create sample”. Pooling can also be applied to extracts and labeled extracts.

No, this is not possible, since there is only one place software is used, namely to register the feature extraction of a scanned image.

Your privileges are not high enough and you have not been granted permission to create hardware types. Contact your BASE administrator. For more information about permissions, please refer to Chapter 24, Account administration.

The most likely explanation is that this particular annotation type has been declared as a protocol parameter. This means that it will only be displayed in BASE if you have used a sample creation protocol which uses that parameter.

In this particular case and because you are using 2 different raw data file formats, you will have to split your experiment in 2. One experiment for those samples processed using Affymetrix platform and another one using Agilent platform. You do not necessarily have to provide all information about the samples again but simply create new raw bioassay data which can be grouped in a new experiment.

Yes it is possible to extend BASE so that it can support your system. You will need to define a new raw data type for BASE by modifying the raw-datatypes.xml configuration file.

Then, you will have to run the updatedb.sh to make the new raw data type available to the system. See Section 21.1, “Upgrade instructions”.

Finally, you will have to configure a raw data import plug-in in order to be able to create rawbioassays. See Section 22.4, “Plug-in configurations” and Section 18.2.2, “Import raw data” for further information.

There is no support for CDT or CAB. Currently only CDF and CEL files are supported by the Affymetrix plug-ins. Annotation files (.csv) are used for uploading probeset (reporter in BASE language) information. The issue of supporting CDT and CAB files is an import and a plug-in issue. There are two ways to solve this:

	Note
	To include CDT and CAB support to BASE, the file formats must be open, that is we must be able to read them without proprietary non-distributable code.

Yes, but not by default. There is an Illumina package that provides Illumina support to BASE. The package is straightforward to install, visit the package site for more information.

Unfortunately this is an "unfixable" defect. The API for unpacking files is a kind of plug-in interface (FileUnpacker) that has been made public. The "mistake" is that the API does not include any information from the file upload dialog except the directory to upload to (not even the file name is included). Introducing new method or parameters will break the API and we prefer to not do that.

As a workaround to this problem the extension of each file is checked against the list of MIME types (Administrate → Types → Mime Types). If a MIME type with the same extension is found and has been connected to a file type, this file type is transferred to the file. This will obviously only work for non-generic file extensions, eg., .gpr for GenePix raw data files, .cel for Affymetrix CEL files, etc.

The BASE development team are working on a plug-in that produces a Tab2Mage file accepted by ArrayExpress. For the plug-in to work properly, a series of rules need to be followed, please refer to Section 18.3.3, “Tab2Mage export” for additional information.

More information about the Tab2Mage format can be found at http://tab2mage.sourceforge.net. To send the submission to array express, use the ArrayExpress FTP site at ftp://ftp.ebi.ac.uk pwd. Log in with username and password aexpress.

	Warning
	The current export plug-in does not support Tab2Mage normalised and transformed files, so some additional work might be required to be fully compliant, please refer to Tab2Mage help notes for creating these final gene expression files and update the Tab2Mage files.

No, not necessarily! Tab2Mage exporter complies with Tab2Mage specifications so you will be Tab2Mage compliant. However, MIAME compliance depends very much on the kind of annotation you have supplied. Please refer to the previous question for more information about how to check for MIAME compliance in BASE using the Experiment overview function.

You can export the data from the tables again. Go to the Raw data tab for each of the raw bioassays you need to export. Use the Export button to export the data. See Section 20.3, “The table exporter plug-in”. for more information.

No, sorry, not for the moment. The Tab2Mage exporter does not support pooling events. We are working on adding this features in future version of the plug-in.

It is possible to trick the system to filter out null values but not non-null values. Use an expression like: ch(1) == 0 || ch(1) != 0. This will match all values, except null values.

Yes, there is. BASE team has created a plug-in based on RMAExpress methods from Bolstad and Irizarry so you can normalise Affymetrix data sets of reasonable size (not 1000 CEL files at a time though even though this might depend on your set-up...) The plug-in is not included in a standard BASE installation, but can be downloaded from the BASE plug-ins web site.

All raw bioassays in the experiment are already imported. In this case the BASE server cannot detect anything to import and returns the somewhat confusing message. Simply add the non-imported raw bioassays to the experiment and try again.