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changes_v1.2_to_v1.3.txt
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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: