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| adjustP2 | Adjust model parameter P2 |
| calibReadMe | View CALIB readme file |
| cbind.ParameterList | Combine RGList\_CALIB, SpikeList or ParameterList objects |
| cbind.RGList_CALIB | Combine RGList\_CALIB, SpikeList or ParameterList objects |
| cbind.SpikeList | Combine RGList\_CALIB, SpikeList or ParameterList objects |
| coerce-method | Red, Green Intensity List - Class |
| dim.RGList_CALIB | Retrieve the Dimensions of an RGList\_CALIB or SpikeList object |
| dim.SpikeList | Retrieve the Dimensions of an RGList\_CALIB or SpikeList object |
| dimnames.RGList_CALIB | Retrieve the Dimension Names of an RGList\_CALIB or SpikeList object. |
| dimnames.SpikeList | Retrieve the Dimension Names of an RGList\_CALIB or SpikeList object. |
| estimateParameter | Estimate model parameter from spikes |
| getColClasses | Construct colClasses vector for use within read.rg function |
| length.RGList_CALIB | Retrieve the Dimensions of an RGList\_CALIB or SpikeList object |
| length.SpikeList | Retrieve the Dimensions of an RGList\_CALIB or SpikeList object |
| merge.RGList_CALIB | Merge RGList\_CALIB or SpikeList objects |
| merge.SpikeList | Merge RGList\_CALIB or SpikeList objects |
| normalizeData | Normalization: estimation of absolute expression levels |
| normdata | Example of normalized data |
| parameter | Calibration Model parameter: ParameterList Example |
| ParameterList-class | Class "ParameterList" - List to store all the parameters |
| plotNormalizedData | plot estimated absolute levels of two conditions |
| plotSpikeCI | plot spike concentration vs measured intensity |
| plotSpikeHI | plot hybridized target vs intensity |
| plotSpikeRG | plot spike intensity R vs G |
| plotSpikeSpotError | plot spot error of spikes. |
| rbind.RGList_CALIB | Combine RGList\_CALIB, SpikeList or ParameterList objects |
| rbind.SpikeList | Combine RGList\_CALIB, SpikeList or ParameterList objects |
| read.rg | Read RGList\_CALIB from Image Analysis Output Files |
| read.spike | Read SpikeList from a RGList\_CALIB and Concentration files |
| RG | Experiment Data: RGList\_CALIB Example |
| RGList_CALIB-class | Red, Green Intensity List - Class |
| show-method | Class "ParameterList" - List to store all the parameters |
| show-method | Red, Green Intensity List - Class |
| show-method | Class "SpikeList" - Spike Intensity and Concentration List |
| spike | Experiment Data: SpikeList Example |
| SpikeList-class | Class "SpikeList" - Spike Intensity and Concentration List |
| [.ParameterList | Subset of RGList\_CALIB, SpikeList or ParameterList object |
| [.RGList_CALIB | Subset of RGList\_CALIB, SpikeList or ParameterList object |
| [.SpikeList | Subset of RGList\_CALIB, SpikeList or ParameterList object |