 |
Page History
| Scrollbar | ||
|---|---|---|
|
Question: What are
...
MAGE-TAB
...
Files?
...
Topic
...
:
...
caArray
...
Usage
...
Release
...
:
...
caArray
...
2.X
...
Date
...
entered
...
:
...
02/12/2009
...
Topics
...
on
...
this
...
page
...
include
...
the
...
following:
...
| Table of Contents |
|---|
...
|
...
|
Answer
MAGE-TAB
...
(MicroArray
...
Gene
...
Expression
...
Tabular)
...
format
...
files
...
refer
...
to
...
simple
...
tab-delimited,
...
spreadsheet-based
...
files,
...
which
...
can
...
be
...
used
...
for
...
annotating
...
and
...
communicating
...
microarray
...
data
...
in
...
a
...
...
...
...
.
...
MAGE-TAB
...
specification
...
is
...
based
...
on
...
the
...
...
...
...
...
Object
...
Model
...
(
...
...
).
...
MAGE-TAB
...
...
and
...
related
...
...
provide
...
more
...
details
...
on
...
the
...
format.
The following table summarizes the definition of each MAGE-TAB format file.
See also #About File Types in caArray.
File Type | File Extension | Description | Processed by caArray | |||||
|---|---|---|---|---|---|---|---|---|
Investigation Description Format (IDF) | .idf | Provides general information about the experiment, including its name, a brief description, the investigator‘s contact details, bibliographic references, and ontologies/databases referenced.
| Yes. Parsed, validated before import | |||||
Sample and Data Relationship Format (SDRF) | .sdrf | An SDRF file describes relationships between samples, arrays, data files, protocols, factor values, etc. Each row in the table represents a hybridization channel, and the columns represent the steps of the experiment, read from left to right. An SDRF contains all of the information linking the samples to your data files, (for example, Affymetrix CEL, Affymetrix CHP). See example in the following figure. | Yes. Parsed, validated before import | |||||
Array Design Format (ADF) | .adf | Defines each array type used. In caArray 2.4, ADF files can be uploaded but they are not parsed. Not required in a caArray experiment. | Can be uploaded, but are not parsed. Vendor-specific ADF files required instead. | |||||
Data Matrix (ADF) | .txt or other | Contains processed array data files in tab-delimited text format. | Only copy number data matrix files parsed |
For more information see MAGE-TAB in caArray--Overview
MAGE-TAB files imported into caARRAY map to data files also imported into the same caARRAY experiment. The following figure illustrates the process.
Building MAGE-TAB Formatted files
Because of the varied nature of every caArray experiment and its corresponding data, it is impossible to outline the exact steps for creating a caArray-compatible MAGE-TAB file. There are strict guidelines, however, for characteristics of MAGE-TAB files that meet the criteria. Refer to Appendix A - MAGE-TAB in caArray in the caArray User's Guide for specific details regarding caArray-compatible MAGE-TAB files. To provide context, see the MAGE-TAB Specification document.
To get started, you can generate a MAGE-TAB template file from EMBL-EBI's MAGE TAB site, or create your own IDF and SDRF files based on the Sourceforge MAGE-TAB documentation.
Be sure and review the details in Appendix A - MAGE-TAB in caArray to ensure that your MAGE-TAB files meet the specifications for compatibility with caArray.
For more information about when to use MAGE-TAB annotation files in caArray, refer to caArray 008 - How do I use the Annotation Tab versus MAGE-TAB Annotation Files in caArray?. For more information on how to upload MAGE-TAB files, refer to Importing MAGE_TAB Files in the caArray User's Guide.
Have a comment?
Please leave your comment in the caArray End User Forum.
| Scrollbar | ||
|---|---|---|
|
