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Documentation · File formats

File formats

Ampliova reads RDML, the open standard for qPCR data, because it carries what the efficiency correction needs: the raw amplification curve of every well.

RDML

An RDML file (.rdml) holds the plate layout, the Cq values and, when exported with them, the raw fluorescence of every cycle. Ampliova reads all three, runs LinRegPCR on the curves through rdmlpython [4], and pre-fills the layout from the sample and target names in the file. Bio-Rad CFX, Applied Biosystems QuantStudio, Roche LightCycler and QIAGEN Rotor-Gene all export it.

Without amplification curves

An RDML file exported without its raw data has Cq values but nothing to fit an efficiency on. Ampliova then analyses the batch with classic ΔΔCq at E = 2, says so in a banner on the results, and records the method that actually ran in every export and in the Methods paragraph. Export again with the curves and re-analyse to get the efficiency correction.

Exporting RDML

QuantStudio (Applied Biosystems)

  1. Open the experiment in Design & Analysis Software.
  2. Go to File → Export and choose RDML.
  3. Check Include amplification data: without it there is no efficiency correction.

Bio-Rad CFX Maestro

  1. Open the run in CFX Maestro.
  2. Go to File → Export → RDML.
  3. Select Include raw fluorescence data and export. The file is a ZIP archive; upload it as it is. CFX names the XML inside after the run rather than rdml_data.xml, which some tools reject; Ampliova reads either.
  4. CFX only writes wells that have a target assigned. Wells left unnamed on the instrument are absent from the file, so assign a target to everything you want analysed.

RT² Profiler arrays

QIAGEN RT² Profiler plates can be uploaded as RDML like any other plate, or as the GeneGlobe export (CSV, TSV or Excel). The gene names embedded in the file fill the layout; when there are none, Ampliova asks for the catalog number and fills the panel’s well-to-gene map from its own table. A GeneGlobe export carries Cq values without amplification curves, so its plates are analysed at E = 2. See the RT² Profiler guide.