The CNCNP and LOHCHP files generated by Genotyping Console software
contain Copy Number and Loss of Heterozygosity (LOH) analysis results
from the CN4 and CN5 algorithms. Copy Number results generated by the CN4 algorithm are retained in
CNCHP filles. LOH results generated by the CN4 algorithm are
stored in LOHCHP files. Copy
Number and LOH results generated by the CN5 algorithm are combined in CNCHP files.
CHP files containing SNP results and CNVCHP files containing Copy Number Variation results
generated by the Genotyping Console software are described in separate documents.
The format of the CNCHP and LOHCHP files
generated by the Genotyping Console software uses the Command Console
binary data format. The following describes the data sets and groups
stored in
the file.
The parameters stored in the header of the file include algorithm
parameters (those whose names are prefixed with "affymetrix-algorithm-param-")
and summary statistics (those whose names are prefixed with "affymetrix-chipsummary-").
These parameters are algorithm specific.
Copy Number Results generated by CN4
The Copy Number analysis results from CN4 are stored in a single
group with a single data set. The data set header will contain a set of
parameters to define the column labels.
The data type identifier is set to: "affymetrix-multi-data-type-analysis"
The data group containing the analysis results is called "MultiData".
The results are stored in a data set named "CopyNumber".
The data set for Copy Number analysis results generated by CN4 will contain the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
|
Chromosome |
UByte. The chromosome display values (1-22, X, Y,
MT) are stored in the data set header. The values presented in this
column are a foreign key to the data set header. The values in this
column are defined as 1-22, 24 (for X), 25 (for Y) and 26 (for MT)
and 255 (for no value) |
|
Position |
UInt |
|
Log2Ratio |
Float |
|
HmmMedianLog2Ratio |
Float |
|
CNState |
UByte |
|
NegLog10PValue |
Float |
|
ChipNum |
UByte |
Loss of Heterozygosity Results generated by CN4
The Loss of Heterozyagosity analysis results from CN4 are stored in a single
group with a single data set. The data set header will contain a set of
parameters to define the column labels.
The data type identifier is set to: "affymetrix-multi-data-type-analysis"
The data group containing the analysis results is called "MultiData".
The results are stored in a data set named "CopyNumber".
The data set for Loss Of Heterozygosity analysis results generated by
CN4 will contain the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
|
Chromosome |
UByte. The chromosome display values (1-22, X, Y,
MT) are stored in the data set header. The values presented in this
column are a foreign key to the data set header. The values in this
column are defined as 1-22, 24 (for X), 25 (for Y) and 26 (for MT)
and 255 (for no value) |
|
Position |
UInt |
|
Call |
UByte |
|
RefCall |
UByte |
|
LohState |
UByte |
|
LohProb |
Float |
|
RetProb |
Float |
|
ChipNum |
UByte |
Copy Number and Loss of Heterozygosity Results Generated by CN5
The Copy Number and Loss of Heterozygosity results generated by CN5 are stored in one file in a single
group with a single data set.
The data set header will contain a set of
parameters to define the column labels.
The data type identifier is set to: "affymetrix-multi-data-type-analysis"
The data group containing the analysis results is called "MultiData".
The results are stored in a data set named "CopyNumber".
The data set for Copy Number and Loss of Heterozygosity results for Genome-Wide
Human SNP Array 6.0 arrays will contain
the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
|
Chromosome |
UByte. The chromosome display values (1-22, X, Y,
MT) are stored in the data set header. The values presented in this
column are a foreign key to the data set header. The values in this
column are defined as 1-22, 24 (for X), 25 (for Y) and 26 (for MT)
and 255 (for no value) |
|
Position |
UInt |
|
CNState |
Float |
|
Log2Ratio |
Float |
|
SmoothSignal* |
Float |
|
LOH |
Float |
|
Allele Difference |
Float |
*Present when smoothed log2 ratios are calculated by the CN5
algorithm |
