4. Data - AlkaBenawra/MDMAPR GitHub Wiki
Data Requirements
A qPCR Experimental Fluorescence File, Standard Curve Fluorescence File, and Metadata File are required in order to use the MDMAPR 2.0 platform.
The Example Data file contains example data files for MIC, StepOnePlus, and Biomeme two3/ Franklin systems.
qPCR Experimental Fluorescence File
In MDMAPR 2.0, qPCR Experimental Fluorescence file refer to the raw fluorescence outputs exported from a qPCR machine which have not been altered or normalized.
Currently, the MDMAPR 2.0 accepts qPCR fluorescence data generated from MIC, StepOnePlus, and Biomeme two3/ Franklin systems. Please note, for the StepOnePlus fluorescence data the MDMAPR 2.0 only processes a single channel of fluorescence (FAM), and currently cannot work with multiplex fluorescence data.
The raw data should be stored as a csv. file or as an Excel spreadsheet as determined by the platform of origin. Users do not need to make any further modifications to the raw dataset before uploading it to MDMAPR.
Standard Curve Fluorescence File
In MDMAPR 2.0, qPCR Standard Curve Fluorescence file refer to the raw fluorescence outputs, used to generate the standard curve, that are exported from a qPCR machine which have not been altered or normalized.
Currently, the MDMAPR 2.0 accepts qPCR fluorescence data generated from MIC, StepOnePlus, and Biomeme two3/ Franklin systems. Please note, for the StepOnePlus fluorescence data the MDMAPR 2.0 only processes a single channel of fluorescence (FAM), and currently cannot work with multiplex fluorescence data.
The raw data should be stored as a csv. file or as an Excel spreadsheet as determined by the platform of origin. Users do not need to make any further modifications to the raw dataset before uploading it to MDMAPR.
Metadata File
To upload data files onto the MDMAPR 2.0 shiny application for analysis, it is required that users fill in a Metadata template file for each qPCR fluorescence file they upload. The Metatdata Template file contains tables to store information related to the project, geographic location, sample collection details, extraction details, assay, taxon, and standard curve.
The Metadata Template contains five tables for data input. These include the project_Table, replicate_Table, results_Table, assay_Table, and standardCurveResults_Table. A full description for each field within the tables can be found in the Metadata Template Column Description document. It is recommended that when users are filling in the Metadata Template they do it in this sequential order: 1)project_Table, 2)replicate_Table, 3)results_Table, 4)assay_Table, and 5)standardCurveResults_Table
1. project_Table
The project table includes fields related to the project, geographic region, site, and station for collected samples.
2. replicate_Table
The replicate table includes fields related to the site conditions for the collected samples, and extracted DNA from the sample.
3. results_Table
The results table includes fields related to each qPCR plate well. A record must be created for each well on the qPCR plate, including blank wells and controls.
4. assay_Table
The assay table includes fields related to the assay used in the experiment and the taxon for the target sample.
5. standardCurveResults_Table
The standard curve results table includes fields related to the qPCR plate wells that were used to create a standard curve for the experiment. A record must be created for each well on the qPCR plate, including blank wells and controls.
Figure 1: The replicate_Table, results_Table, and standardCurveResults_Table include foreign keys that relate their information back to other tables. The results_Table contains the foreigns keys assay ID from the assay_Table and extractID from the replicate_Table. The assayID used in the results_table must exist in the assay_Table and the extractID used must exist in the replicate_Table. The standardCurveResults_Table contains the foreign key assayID from the assay_Table and this key must exist in the assay_Table. Lastly, the replicate_Table contains the foreign key stationID from the project_Table and this key must exist in the project_Table.