Changes between RDML v1.2 to v 1.3 Digital PCR measure a high number of partitions. To not overload the XML file with this data, separate table files are used that are stored in a partitions folder within the RDML zip file. The counts of the partitions must be stored in the XML file within the corresponding data elements. The table files must use tabs (\t) as column separators and dots (.) as decimal separators. A line must contain the data of one partition. For each fluorescence two columns are created. One with the endpoint fluorescence value and a second with its score. The score can be: u - undefined or not yet scored p - positive n - negative e - excluded (should be ignored) The file must have a header line with the target ids matching the fluorescence value. The first lines could look like: GAPDH\tGAPDH\tHBV\tHBV\n 3412.32\tp\t121.89\tn\n 239.23\tn\t3459.27\tp\n ----------------------------------------------------------------------------- Changes on the RDML XML structures: - reactType data: The element can now occur 0(!) to unlimited times. As data can also be in the partitions element, there can be RDML files without data elements. partitions: The new element can occur 0 to one times. Reactions split up in partitions as in digital PCR must report data using this elements. - partitionsType volume: New element This element contains the average volume of one partition in nanoliter (nl). endPtTable: New optional element This element contains the filename string. See fist section. data (partitionDataType): The element can occur 1 to unlimited times. As data can also be in the partitions element, there can be RDML files without data elements. - partitionDataType tar: New element The target id. excluded: New optional element If present, the data element should be excluded. It should contain a string explaining the reason for exclusion. Several reasons for exclusion should be seperated by semicolons ";". note: New optional element A note string similar to "excluded". It may contain a string with notes to the data element which do not lead to exclusion of the entry. Several notes should be seperated by semicolons ";". pos: New element Positive partitions - The number of positive partitions. neg: New element Negative partitions - The number of negative partitions. undef: New optional element Undefined partitions - The number of undefined or not yet scored partitions. excl: New optional element Excluded partitions - The number of excluded partitions. conc: New optional element Concentration - The concentration in copies per microliter reaction mix. - dataType ampEffMet: New element Amplification efficiency method as free text. N0: New element Pronounced N-zero. Target quantity or starting concentration per reaction, expressed in calculated arbitrary fluorescence units. Negative values are used to express following conditions: Not Available: -1.0 ampEff: New element Amplification efficiency should as the fold-increase of DNA per cycle (the base of the exponential function), for example 1.95 for 95% efficiency. If absent, the ideal efficiency of 2.0 should be used for calculations. ampEffSE: New element The standard error of the value provided in "ampEff" should be given. corrF: New element The correction factor indicating the fraction of the expected product in all products. A factor of 0.25 indicates that the expected product contributes only a quarter to the observed results. corrN0 = (N0 * corrF) / corrP If absent, the ideal correction factor of 1.0 should be used for calculations. corrP: New element The correction factor to correct for inter run differences within this experiment. corrN0 = (N0 * corrF) / corrP If absent, the ideal correction factor of 1.0 should be used for calculations. Negative values are used to express following conditions: Not Available: -1.0 corrCq: New element Corrected quantification cycle - The corrected calculated fractional PCR cycle used for downstream quantification. Negative values are used to express following conditions: Not Available: -1.0 meltTemp: New element The melting temperature in degrees Celsius of the amplified amplicon. note: New element A note string similar to "excl". It may contain a string with notes to the data element which do not lead to exclusion of the entry. Several notes should be seperated by semicolons ";". - targetType meltingTemperature: New optional element The melting temperature in degrees Celsius of the amplified amplicon. - dyeType dyeChemistry: New optional element The monitoring chemistry of this dye. The options are: - non-saturating DNA binding dye (SYBR Green I) - saturating DNA binding dye (Eva Green, LC Green Plus, BEBO, Syto9) - hybridization probe (Molecular Beacon, Light-Up probes, BHQnova Probe) - hydrolysis probe (TaqMan, NuPCR) - labelled forward primer (LUX primer) - labelled reverse primer (Scorpion probe, Sunrise probe, Amplifluor Universal detection system) - DNA-zyme probe (QZyme probe) - sampleType type: Uses new element sampleTargetType and can occur 0 to unlimited times. The same sample could have the sampleTypeType pos for one target and ntp for a different target. Therefor several entries are allowed and can be linked to a target. If no target is given, only one entry should be present valid for all targets in this run. If the element type is absent, the sample type is "unkn" (default value). quantity: The element can occur 1 to unlimited times. It can have the target as attribute targetId. The same sample could have the quantityType 1000 copies per microliter for one target or 1 fold for all targets. Optical calibrators work independent of targets. Therefor several entries with or without target are allowed and can be linked to a target. ----------------------------------------------------------------------------- Clarifications of existing elements without functional changes: