Chapter 32. Frequently Asked Questions with answers

Table of Contents

32.1. Reporter related questions with answers
32.2. Array design related questions with answers
32.3. Biomaterial, Protocol, Hardware, Software related questions with answers
32.4. Data Files and Raw Data related questions with answers
32.5. Analysis related questions with answers

This chapter presents a list of solutions to common problems and tasks in BASE. The information is is collected from the mailing lists, private communication, and from issues frequently encountered in BASE introduction courses. If you have BASE solutions that should be added to this chapter please contact us through the usual communication channels, see Chapter 3, Resources for contact information.

32.1. Reporter related questions with answers

Q: My favourite database is not used for annotating reporters. Can I add my database to BASE and if so, how should it proceed?
Q: I have made a mistake while loading my reporters. How can I delete them all in one go ?
Q: I get a message "Error: Unable to import root bioassay. Item not found: Reporter[externalId=AFFX-2315060]" when I try to create a root bioassayset.
Q:

My favourite database is not used for annotating reporters. Can I add my database to BASE and if so, how should it proceed?

A:

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 21.2, “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 and extensions.

Q:

I have made a mistake while loading my reporters. How can I delete them all in one go ?

A:

The reporter import plug-in can be executed in delete mode. Run the plug-in again and select the same file you used 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.

Q:

I get a message "Error: Unable to import root bioassay. Item not found: Reporter[externalId=AFFX-2315060]" when I try to create a root bioassayset.

A:

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 9.2.1, “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.

32.2. Array design related questions with answers

Q: What it the best way to create an array design in BASE when starting from a GAL file?
Q: I am confused. What is the difference between Reporter map importer, Print map importer and Reporter importer?
Q:

What it the best way to create an array design in BASE when starting from a GAL file?

A:

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

  1. Define the features of an array design for a non-Affymetrix platform using the Reporter Map importer plug-in.

    To do so, after having created an new array design, go to the single-item view by of the newly created array design. Click on the Import the button. If you do not see it, it means that you have not enough privileges (contact the administrator).

    This starts the plug-in configuration wizard. Select the auto detect option and in the next step your GAL file.

    Now, there is the risk that no file format has been defined for GAL files. This must be done by an administrator or other user with proper privileges. See Section 22.2, “Plug-in configurations” for information about this.

    Once done (and if everything went fine), you can see from the Array Design list view that the Has features entry has been modified and is set to 'Yes (n)' where n indicates the number of spots (features) for this array.

    [Note] Note

    Features can also be loaded from a Genepix GPR file with the same procedure.

  2. Define the Reporters present on the array design using the Reporter importer plug-in.

    To do so, Go to ViewReporters and click on Import. This starts a Reporter Importer plug-in

    More information about importing Reporters can be found in Chapter 9, Reporters

Q:

I am confused. What is the difference between Reporter map importer, Print map importer and Reporter importer?

A:

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.

32.3. Biomaterial, Protocol, Hardware, Software related questions with answers

Q: I have just created a new item but I can not see it. Am I doing something wrong?
Q: I can only see XX columns in the list view but I know I have a lot more information. Is there a way I can customise the column display?
Q: Is it possible to sort the values in a column in the list view?
Q: Is it possible to sort the annotation types from Annotation & parameters tab in the single-item view?
Q: I have to create pools of samples in my experiment due to scarcity of the biological material. Can I represent those pooled samples is BASE?
Q: I need to create a new item subtype but the New… button is grey and does not work. Why?
Q: I have created an Annotation Type Temperature and shared it to everyone but when I want to use it for annotating a sample, I can not find it! How is that?
Q: I have carried out an experiment using both Affymetrix and Agilent arrays but I can not select more than one raw data type in BASE. What should I do?
Q:

I have just created a new item but I can not see it. Am I doing something wrong?

A:

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.

Q:

I can only see XX columns in the list view but I know I have a lot more information. Is there a way I can customise the column display?

A:

Yes, you can display many more columns. See Section 5.4.3, “Configuring which columns to show”.

Q:

Is it possible to sort the values in a column in the list view?

A:

Of course it is. See Section 5.4.1, “Ordering the list”.

Q:

Is it possible to sort the annotation types from Annotation & parameters tab in the single-item view?

A:

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

Q:

I have to create pools of samples in my experiment due to scarcity of the biological material. Can I represent those pooled samples is BASE?

A:

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 16.2.1, “Create sample”. Pooling can also be applied to extracts.

Q:

I need to create a new item subtype but the New… button is grey and does not work. Why?

A:

Your privileges are not high enough and you have not been granted permission to create subtypes. Contact your BASE administrator. For more information about permissions, please refer to Chapter 23, Account administration.

Q:

I have created an Annotation Type Temperature and shared it to everyone but when I want to use it for annotating a sample, I can not find it! How is that?

A:

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.

Q:

I have carried out an experiment using both Affymetrix and Agilent arrays but I can not select more than one raw data type in BASE. What should I do?

A:

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.

32.4. Data Files and Raw Data related questions with answers

Q: It seems that BASE does not support the data files generated by my brand new scanner. Is it possible to add it to BASE?
Q: Are Affymetrix CDT and CAB files supported by BASE?
Q: Are Illumina data files supported by BASE?
Q:

It seems that BASE does not support the data files generated by my brand new scanner. Is it possible to add it to BASE?

A:

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 22.2, “Plug-in configurations” and Section 18.2.3, “Import raw data” for further information.

Q:

Are Affymetrix CDT and CAB files supported by BASE?

A:

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:

  1. Write code that treats the files in a proper way and submit the solution to the developer team (preferred route).

  2. Submit a ticket through http://base.thep.lu.se explaining what you'd like to see with respect to to CDT and CAB files.

[Note] 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.

Q:

Are Illumina data files supported by BASE?

A:

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.

32.5. Analysis related questions with answers

Q: Is it possible to use the formula filter to filter for null values (or non-null values)?
Q: OK, I have uploaded 40 CEL files in BASE but are there any tool to perform normalisation on Affymetrix raw data?
Q: I am trying to import raw bioassays using the import button in the experiment properties view but BASE claims that Could not find any plugins that you have permission to use. I know there are import plug-ins available to me since I have successfully imported data before, why does the import fail?
Q:

Is it possible to use the formula filter to filter for null values (or non-null values)?

A:

Yes, use an expression like: ch(0) != null. This will match all values, except null values.

Q:

OK, I have uploaded 40 CEL files in BASE but are there any tool to perform normalisation on Affymetrix raw data?

A:

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.

Q:

I am trying to import raw bioassays using the import button in the experiment properties view but BASE claims that Could not find any plugins that you have permission to use. I know there are import plug-ins available to me since I have successfully imported data before, why does the import fail?

A:

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.