inst/RDMLedit/md/help.md

In RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

rdmlEdit allows viewing, editing, merging and creating files in RDML format. It can be accessed as a web server (http://shtest.evrogen.net/rdmlEdit/) or deployed locally using rdmlEdit() function.

GUI consists of five tabs:

• Files: basic file operations:
  • import data (different file formats supported),
  • merge several files into one,
  • review structure of files,
  • save RDML file.
• Metadata: modifications of RDML metadata (e.g., information about experimenter, samples, targets).
• qPCR: raw qPCR curve data.
• Melting: raw melting curve data.
• Help: this very page.

The exemplary .RDML files are available in the repository of RDML package: https://github.com/kablag/RDML/tree/master/inst/extdata.

Files

Upload file(s)

Upload one or more files. Supported formats:

• .rdml or .lc96p -- RDML files generated by Bio-Rad CFX96, Roche LightCycler 96 and Applied Biosystems StepOne.
• .csv -- file that contains first column cyc for qPCR data or tmp for melting data. Other columns -- fluorescence signal. Column names become sample names.
• .xls -- file generated by ABI 7500 v.2 software which contains \code{Sample Setup} and \code{Multicomponent Data} sheets. To do this use File>Export...; check Sample Setup and Multicomponent Data; select One File; click Start Export.
• .xlsx -- file containing description sheet and qPCR data located in adp and/or mdp sheet.

Example structure of sheets in .xslx file:

description

Contains description of experiments. Column names have to be exactly the same as in the example.

| fdata.name | exp.id | run.id | react.id | sample | target | target.dyeId | |------------|--------|--------|----------|-----------------|--------|--------------| | D1 | exp1 | run1 | 1 | D1 - Stock cDNA | MLC-2v | Cy5 | | D2 | exp1 | run2 | 1 | D2 - 1/10 cDNA | MLC-2v | Cy5 | | D3 | exp1 | run3 | 1 | D3 - 1/100 cDNA | MLC-2v | Cy5 |

adp

Contains qPCR fluorescence data. Column names link to the fdata.name at description.

| cyc | D1 | D2 | D3 | |-----|--------------|--------------|--------------| | 1 | 0.1460399771 | 0.1479223401 | 0.1474461126 | | 2 | 0.1520586393 | 0.1482665679 | 0.147808717 | | 3 | 0.1513144293 | 0.1489176364 | 0.1483215208 | | 4 | 0.1525136885 | 0.1493655183 | 0.1487343487 | | 5 | 0.1539632217 | 0.150546809 | 0.1490988961 |

mdp

Contains melting fluorescence data. Column names link to the fdata.name at description.

| tmp | D1 | D2 | D3 | |-----|------|------|------| | 20 | 3401 | 3595 | 3656 | | 21 | 3388 | 3575 | 3634 | | 22 | 3374 | 3555 | 3613 | | 23 | 3361 | 3535 | 3592 | | 24 | 3348 | 3515 | 3570 |

View File

Uploaded file(s) can be viewed by selecting its name at View File selector. After this dendrogram with file structure should appear at the bottom of the page.

Merge RDMLs

You can merge several RDML files into one by selecting RDMLs in Merge RDMLs field. Selected RDMLs will be merged into RDML selected in View File selector. Click Merge to proceed merging.

Date Made and Date Updated

RDML metadata fields.

Remove RDML

Removes uploaded RDML file.

Update

Saves all changes made to RDML. Click this button before downloading edited file!!!

Download RDML

Download currently selected RDML object as compressed RDML v1.2 file.

Metadata

Description of metadata fields can be found in RDML v1.2 format description or in the RDML package help to corresponding classes. Input to any field is validated by RDML classes. For example you cannot input text where number is needed. All errors print to the log at the bottom of the page.

All list elements (i.e. Sample) can be selected by corresponding selector. A new element can be added by writing its name in selector. To remove element, click Remove ... at the bottom of the list element editor.

qPCR

Access raw qPCR curves. To view one (or more) curve, click on curve at the table with curves description. To view all curves again -- deselect descriptions. Curves arn't preprocessed and editable!

Melting

Access raw melting curves. To view one (or more) curve, click on curve at the table with curves description. To view all curves again -- deselect descriptions. Curves are not preprocessed or editable!

Further information and R packages

The rdmlEdit function can be used to manage qPCR data. However, there are further R packages which can be used to preprocess raw data, analyze qPCR and melting curve data, impute missing values or perform gene expression analysis. More information can be found in dedicated studies. Quality management of qPCR data is an important aspect of the whole analysis pipeline. For example the preprocessing by smoothing can alter the Cq value and estimates of the amplification efficiency. Moreover, selected qPCR devices introduce a systematic periodicity into the Cq data which can be tested by an indepentent Periodicity shiny GUI.

RDML documentation built on June 25, 2019, 5:03 p.m.