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Highlights for Building caArray's MAGE-TAB Annotation =
Files
Topic: caArray Usage
Release: Up to caArray 2.2
Date entered: 02/17/2009
Introduction
caArray has been designed to handle MAGE-TAB data using certain conventi=
ons. The caA=
rray User Guide devotes a section in Chapter 7 =E2=80=93 Submitting Dat=
a to Importing MAGE-TAB and an =
entire appen=
dix to working with MAGE-TAB files in caArray. The appendix specificall=
y includes much specific detail from recognized data fields to validation r=
ules essential for importing MAGE-TAB files. Highlights are outlined below =
to offer you a quick start.
Recognized Fiel=
ds and Validation Rules for MAGE-TAB Annotation Files
- You can describe your experiment in great detail with the convenience o=
f managing MAGE-TAB files in spreadsheet format. For example, a biomaterial=
(source, sample, extract, or labeled extract) named in one column can be f=
ollowed by any number of characteristics columns containing annotation data=
about that biomaterial.
It should be noted that caArray has requirements about which fields should=
be used and the order in which they must be listed. For example, in an SDR=
F file, the biomaterials columns must follow the order of Source Name - Sam=
ple Name - Extract Name - Labeled Extract Name. See Biomaterial Column Order in an SDRF.
- Controlled vocabularies should be used in IDF and SDRF files. The commo=
nly used vocabularies can be found in MGE=
D Ontology (MO) or the NCI Thesaurus. Each TERM SOUR=
CE REF should have an entry in the IDF file. If term source is unknown, use=
"caArray" in the TERM SOURCE REF column. See Term Source REF.
- All column types are not mandatory in the SDRF. caArray can auto-generate missing biomaterials =
and associate protocols intelligently.
For a detailed list of recognized fields and validation rules for IDF an=
d SDRF files, refer to Appendix A in the User's Guide.
MAGE-TAB Files: Upload and Import
See Importing MAGE-TAB Data =
in the caArray User's Guide for more information about all points noted in =
this section.
- MAGE-TAB Files must be imported into experiments. That is, an experimen=
t needs to be created before MAGE-TAB files are imported.
- Although only one IDF is allowed per import session, multiple IDF files=
are allowed per experiment.
- IDF, SDRF(s), data file(s) referenced in SDRF files must be validated a=
nd imported together.
- Data files that are not referred to by SDRF files can also be imported =
into the same experiment, but they must be uploaded, validated and imported=
in a separate session from IDF/DSRF files.
- MAGE-TAB ADF and Data Matrix files can be uploaded, but caArray does no=
t parse these files. the exception is copy number data matrix files, which =
caArray does parse. See About Fi=
le Types in caArray.
SDRF File Has Higher Priority
Annotations can be configured via the Annotations tab in caArray or via =
an SDRF file (Annotations Tab vs. MAGE-TAB Annotation Files in caArray). The design=
ation in the SDRF is authoritative. For example: The tissue site for one sa=
mple is set to be "Lung" from the annotation interface, but it is set to be=
"Brain" in the SDRF file. Upon data upload, the tissue site will be shown =
as "Brain", since SDRF file has higher priority than "Annotation" interface=
. See SDRF Decides Raw versus D=
erived Data File.
Known Bug List in caArray
Known Bug List for MAGE-TAB Files
Error Message |
Known Bugs |
"Term Source Ref is not preceded by valid dat=
a type" |
Factor Value can not have "Term Source REF" f=
ollowed |
Further Readings on MAGE-TAB Files
Have a comment?
Please leave your comment in the caArray End User Forum.
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