caseof1R2G

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Description

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

Usage

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caseof1R2G(centerR, centerG, origImg, chaImgs, minDiff, despeckle, ImgLimits,
  BFarea, chip.type, separator, image.type, show.possible.contamination)

Arguments

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.

Value

A list of location estimates

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