mergeScansRG(RGlow, RGhigh, AboveNoiseLowG=NULL, AboveNoiseLowR=NULL, outlierp=0.01)RGList containing red and green intensities constituting two-color microarray data scanned at a lower gain setting.RGList containing red and green intensities constituting two-color microarray data scanned at a higher gain setting.RGList-class with the following components:Gsaturated, Rsatured, Goutlier and Routlier.
The first two contain saturation flags (1=saturated, 0=otherwise) for the green (cy3) and red (Cy5) channels of the high scan.
The second two contain outlier flags (1=outlier, 0=otherwise) for the green (cy3) and red (Cy5) channels.Each fluorescent label on a two-color array can be scanned twice: for example, a high scan targeted at reaching saturation level for the brightest 1 percent of the spots on the array, and a low scan targeted at the lowest level of intensity which still allowed accurate grid placement on the arrays. By merging data from two separate laser scans of each fluorescent label on an array, we can avoid the potential bias in signal intensities due to below noise or above saturation and, thus provide better estimates of true differential expression as well as increase usable spots.
The merging process is designed to retain signal intensities from the high scan except when scanner saturation causes the high scan signal to be under-measured. The saturated spots are predicted from the corresponding low scans by the fitted regression model. It also checks any inconsistency between low and high scans.
## Not run:
# #RG1: An RGList from low scan
# #RG2: An RGList from high scan
# RGmerged <- mergeScansRG(RG1,RG2,AboveNoiseLowG=ANc3,AboveNoiseLowR=ANc5)
#
# #merge two scans when all spots are above noise in low scan and no outlier detection.
# RGmerged <- mergeScansRG(RG1,RG2,outlierp=0)
# ## End(Not run)
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