caseof2R1G: caseof2R1G
In CONFESS: Cell OrderiNg by FluorEScence Signal

It processes the case of >1 spots in the red channel and 1 spot in the green channel. BF image modelling is not necessarily performed. It reports possible contamination.

1
2
3

caseof2R1G(centerR, centerG, origImg, chaImgs, minDiff, despeckle,
  ImgLimits, BFarea, chip.type, separator, image.type,
  show.possible.contamination)

`centerR`	Data matrix. The location statistics of one channel.
`centerG`	Data matrix. The location statistics of the other channel.
`origImg`	Data matrix. The original BF image to be read and processed.
`chaImgs`	List. The channel image data (data matrices) of a sample.
`minDiff`	Float. the mu_hat of the H0: image-to-noise ratio = log(foreground_signal) - log(background_signal) = mu_hat. Rejection of H0 implies that the identified spot is brighter than background. Default is 0.5.
`despeckle`	Logical. If TRUE the BF image is despeckled.
`ImgLimits`	Integer. It instructs the algorithm to find spots in the specified central image area. For example, for a 512 x 512 image with cutSides = 50, it will search for spots in the central area [cutSides:(512-ImgLimits),ImgLimits:(512-ImgLimits)] of the image matrix.
`BFarea`	Integer. Defines a rectangular pseudo-spot size whose fluorescence will be estimated. This is mainly used in BF image modeling where a fluorescence spot could not be originally detected. The value of this parameter is also used as a cut-off to find matched spots across channel of the same sample image.
`chip.type`	Character string. It specifies the type of Fluidigm chip to be analyzed.
`separator`	Character string. Removes the Bright Field ("BF") and channel indicators (IDs) from the image file names.
`image.type`	Character string. A triplet of IDs to characterize the type of images under study.
`show.possible.contamination`	Logical. If TRUE it reports all identified unmatched spots in both channels.