Table of Contents
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.
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 |
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. |
Q: |
What it the best way to create an array design in BASE when starting from a GAL file? |
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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
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Q: |
I am confused. What is the difference between Reporter map importer, Print map importer and Reporter importer? |
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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. |
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 Section 16.2.1, “Create sample”. Pooling can also be applied to extracts. button. For more information see |
Q: |
I need to create a new item subtype but the 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 |
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. |
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? |
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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
Then, you will have to run the 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. |
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Q: |
Are Affymetrix CDT and CAB files supported by BASE? |
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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:
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Q: |
Are Illumina data files supported by BASE? |
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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. |
Q: |
Is it possible to use the formula filter to filter for
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A: |
Yes, use an expression like:
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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. |