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MAGE-TAB and Tab2MAGE: a comparison |
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MAGE-TAB is a new data format, designed by members of the microarray community as a simplified standard representation format for microarray data. In contrast, Tab2MAGE is an older, simplified tabular format developed by ArrayExpress some years ago. In most cases these two formats can be used interchangeably, but there are a number of situations in which one or the other may have an advantage. As a rule, anything that can be expressed in Tab2MAGE can also be described in MAGE-TAB, but not vice versa. This is because MAGE-TAB extends the ideas behind Tab2MAGE to give it a far greater flexibility and scope.
We have created a Tab2MAGE to MAGE-TAB converter tool which is now available for download here.
Below is a table summarising the strengths and weaknesses of these two tabular formats:
| Tab2MAGE | MAGE-TAB | |
|---|---|---|
| Simpler to use for array-based gene expression data (4) | Yes | No |
| Can be annotated with ontology term accession and source (1) | No | Yes |
| Supports metabolomic and proteomic data (2) | No | Yes |
| Supports high-throughput sequencing data (2) | No | Yes |
| Experiment must follow a standard, predefined scheme (3) | Yes | No |
| Column ordering is flexible (4) | Yes | No |
| Columns with the same name can appear more than once (4) | No | Yes |
| Tries to "Do What You Mean" (4) | Yes | No |
| Forces consistency of internal references (4) | No | Yes |
| Supported by other members of the microarray community | No | Yes |
1. While Tab2MAGE allows (and encourages) the use of ontology terms to annotate your data, it provides no means to include the source of these terms, or formal identifiers/accessions. MAGE-TAB corrects this by adding "Term Source REF" and "Term Accession Number" fields to help capture this information.
2. Tab2MAGE was developed solely to describe microarray experiments, and as such the concept of "hybridization" is central. MAGE-TAB has been extended to encompass other kinds of biological assay, enabling the user to describe data from multiple technologies (e.g., proteomics, metabolomics, high-throughput sequencing) in a single document.
3. Tab2MAGE assumes that your experiment is a standard microarray hybridization study, and that your sample processing followed a defined series of steps: Source -> Sample -> Extract -> Labeled Extract -> Hybridization (for ChIP-chip experiments an Immunoprecipitate step may also be used). In contrast, MAGE-TAB allows you to create sample processing schemes of arbitrary complexity.
4. While increasing the flexibility of the tabular format, MAGE-TAB has sacrificed some ease-of-use. For example, while the columns in a Tab2MAGE spreadsheet can be ordered in whichever way suits you, MAGE-TAB constrains this order to follow the steps performed in the experiment. That is, columns in a MAGE-TAB SDRF must be ordered left-to-right in chronological order of execution. MAGE-TAB also forces you to be explicit about all the steps of your experiment, while Tab2MAGE will attempt to infer what was done from a minimal subset of spreadsheet columns. Finally, there are several places in a MAGE-TAB SDRF document which may refer back to elements defined in the IDF, and these must be internally consistent. No such requirement is made for Tab2MAGE documents.
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