The DMET.CHP files generated by the DMET Console software contain
genotyping and copy number analysis results generated by the DMET
algorithm.
The format of the DMET.CHP file generated by the DMET Console software is the Command Console
binary data format.
The generic data header will include a file type identifier set to: "affymetrix-multi-data-type-analysis"
The parameters stored in the header of the file include algorithm
parameters (those whose names are prefixed with "affymetrix-algorithm-param-opt-")
and summary statistics (those whose names are prefixed with "affymetrix-chipsummary-").
These parameters are algorithm specific.
The analysis results from the DMET algorithm are stored in a single
data group with three data sets. The data group containing the data sets with the analysis results is called "MultiData".
Biallelic genotyping results are stored in a data set named "DmetBiallelic". Multiallelic genotyping
results are stored in a data set named "DmetMultiAllelic. The results of copy number analysis are stored in a data set named "DmetCopyNumber".
Each of the data set headers will contain a set of parameters to define the column labels
retained in the data set.
The abstract allele codes A-F can be decoded for a given ProbeSetName via a lookup of the
DMET_Plus marker annotations on NetAffx (Allele Code -> Reported Strand Alleles)
The content of of the data sets is detailed in the following
sections.
Biallelic Genotyping Results
Biallelic Genotyping results are stored in a data set named "DmetBiAllelic".
The data set contains a the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
| Call |
UByte (see the table below for possible values) |
|
Confidence |
Float |
| ForcedCall |
UByte (see the table below for possible values) |
| Signal A |
Float |
| Signal B |
Float |
| Context A |
UByte (always 255) |
| Context B |
UByte (always 255) |
The possible values for the Call and ForcedCall columns are as follows:
| Call Code |
Call |
| 16 |
No Call* |
| 17 |
ZeroCopyNumber |
| 18 |
A |
| 19 |
B |
| 25 |
A/A |
| 26 |
A/B |
| 32 |
B/B |
| 254 |
PossibleRareAllele* |
| 255 |
NotAvailable |
* Call only
Multiallelic Genotyping Results
Multiallelic Genotyping results are stored in a data set named "DmetMultiAllelic".
The data set contains a the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
| Call |
UByte (see the table below for possible values) |
|
Confidence |
Float |
| ForcedCall |
UByte (see the table below for possible values) |
| AlleleCount |
UByte |
| Signal A |
Float |
| Signal B |
Float |
| Signal C |
Float |
| Signal D |
Float |
| Signal E |
Float |
| Signal F |
Float |
| Context A |
UByte (always 255) |
| Context B |
UByte (always 255) |
| Context C |
UByte (always 255) |
| Context D |
UByte (always 255) |
| Context E |
UByte (always 255) |
| Context F |
UByte (always 255) |
The possible values for the Call and ForcedCall columns are as follows:
| CHP Call Code |
Call |
| 16 |
No Call* |
| 17 |
ZeroCopyNumber |
| 18 |
A |
| 19 |
B |
| 20 |
C |
| 21 |
D |
| 22 |
E |
| 23 |
F |
| 25 |
A/A |
| 26 |
A/B |
| 27 |
A/C |
| 28 |
A/D |
| 29 |
A/E |
| 30 |
A/F |
| 32 |
B/B |
| 33 |
B/C |
| 34 |
B/D |
| 35 |
B/E |
| 36 |
B/F |
| 38 |
C/C |
| 39 |
C/D |
| 40 |
C/E |
| 41 |
C/F |
| 43 |
D/D |
| 44 |
D/E |
| 45 |
D/F |
| 47 |
E/E |
| 48 |
E/F |
| 50 |
F/F |
| 254 |
PossibleRareAllele* |
| 255 |
NotAvailable |
* Call only
Copy Number Results
Copy Number results are stored in a data set named "DmetCopyNumber".
The data set contains a the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
| CN Call |
Short (* see the table below for possible values) |
|
CN Confidence |
Float (-2 when not available) |
| CN_force |
Short (+ see the table below for possible values) |
| CN_estim |
Float (-2 when not available) |
| CN_lower |
Float (+ see the table below for possible values) |
| CN_upper |
Float (+ see the table below for possible values) |
* The possible values for the CN Call column are:
| Call Code |
Call |
| 0 |
ZeroCopyNumber (copy number = 0) |
| -1 |
No Call* |
| -2 |
Not Available |
| -3 |
OneOrMore (copy number is >= 1) |
+ The possible values for the CN_force, CN_lower and CN_upper are:
| Call Code |
Call |
| 1 |
copy number state = 1 (in a two state model) |
| 0 |
copy number state = 0 (in a two state model) |
| -2 |
Not Available |
| 
