Note that if you made any preprocession all fluorescence points will be overwritten with the new calculated values!!!
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:
The exemplary .RDML files are available in the repository of RDML package: https://github.com/kablag/RDML/tree/master/inst/extdata.
Upload one or more files. Supported formats:
Example structure of sheets in .xslx file:
Contains description of experiments. Column names have to be exactly the same as in the example.
|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|
Contains qPCR fluorescence data. Column names link to the fdata.name at description.
Contains melting fluorescence data. Column names link to the fdata.name at description.
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.
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.
RDML metadata fields.
Removes uploaded RDML file.
Saves all changes made to RDML. Click this button before downloading edited file!!!
Download currently selected RDML object as compressed RDML v1.2 file.
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.
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!
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!
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.