Affymetrix® Genotyping Console CNCHP and LOHCHP Data File Formats
CNCHP AND LOHCHP FILES
Description
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 files. 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.
Format
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