Affymetrix® Expression Console CHP Data File Format
CHP FILE
Description
The CHP files generated by the Expression Console software contain probe set analysis results from the MAS5, PLIER, RMA and DABG algorithms.
Format
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 generic data header shall include:
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.
MAS5 Results
The analysis results from the MAS5 algorithm are stored in a file with a single group with a single data set. The data set header will contain a set of parameters to define the column labels. See the MAS5 Statistical Algorithm Description document on the Affymetrix web site for a description on each metric.
The data type identifier is set to: "affymetrix-expression-probeset-analysis"
The data group containing the analysis results is called "Expression Results". It contains a single data set, also called "Expression Results", containing the analysis results. The data set contains the following columns.
| Column Name | Column Type |
|---|---|
| Probe Set Name | Ascii |
| Detection | UByte (0 = present, 1 = marginal, 2 = absent, no call otherwise) |
| Detection p-value | Float |
| Signal | Float |
| Number of Pairs | UShort |
| Number of Pairs Used | UShort |
A second data group provides storage for the background zone information. This is the background value computed by the MAS5 algorithm on a per zone basis. The data set header will contain a set of parameters to define the column labels.
The data group name is called "Background Zone Data". It contains a single data set, also called "Background Zone Data", containing the background values for each zone. The data set contains the following columns.
| Column Name | Column Type |
|---|---|
| Center X | Float |
| Center Y | Float |
| Background | Float |
| SmoothFactor | Float |
RMA/PLIER Results
The analysis results from the RMA or PLIER algorithms are stored in file with a single group with a single data set. The data set header will contain a set of parameters to define the column labels. See the MAS5 Statistical Algorithm Description document on the Affymetrix web site for a description on each metric.
The data type identifier is set to: "affymetrix-quantification-analysis"
The data group containing the analysis results is called "Quantification". It contains a single data set, also called "Quantification", containing the analysis results. The data set contains the following columns.
| Column Name | Column Type |
|---|---|
| ProbeSetName | Ascii |
| Quantification | Float |
PLIER with DABG Results
The analysis results from the PLIER with DABG (detected above background) algorithms are stored in file with a single group with a single data set. The data set header will contain a set of parameters to define the column labels. See the MAS5 Statistical Algorithm Description document on the Affymetrix web site for a description on each metric.
The data type identifier is set to: "affymetrix-quantification-detection-analysis"
The data group containing the analysis results is called "QuantificationDetection". It contains a single data set, also called "QuantificationDetection", containing the analysis results. The data set contains the following columns.
| Column Name | Column Type |
|---|---|
| ProbeSetName | Ascii |
| Quantification | Float |
| Detection | Float |