The CHP files generated by the Genotyping Console software contain SNP analysis results
from the Birdseed and BRLMM genotyping algorithms .
CNCHP and LOHCHP files containing Copy Number
and Loss of Heterozygosity results generated by the Genotyping Console software are
described in a separate document. CNVCHP files containing
Copy Number Variation Results generated by the Genotyping Console
software are also described in a separate document.
The format of the CHP file
generated by the Command 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-parameter-")
and summary statistics (those whose names are prefixed with "affymetrix-chipsummary-").
These parameters are algorithm specific.
SNP Results
The analysis results from the SNP algorithms 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".
For the SNP results, these are stored in a data set named "Genotype".
The data set contains a the following columns:
| Column Name |
Column Type |
| ProbeSetName |
Ascii |
| Call |
UByte (6 = AA, 7 = BB, 8 = AB, no
call otherwise) |
|
Confidence |
Float |
| ForcedCall |
UByte (6 = AA, 7 = BB, 8 = AB) |
| SignalA+ |
Float |
| SignalB+ |
Float |
| Contrast* |
Float |
| Strength* |
Float |
+ The signal A and B values are stored for the birdseed algorithm.
* The contrast and
strength values are stored for the BRLMM algorithm.
| 
