estParamFlowVS: Estimate optimum parameters for per-channel within-population...
In flowVS: Variance stabilization in flow cytometry (and microarrays)

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/flowVS.R

This function estimates the variance stabilizing cofactors, one for each channel for the entire dataset. When a fluorescence channel z is transformed by asinh transformation with the optimum cofactor for z, the within-population variances of populations from all samples in the channel z are approximately stabilized.

1	estParamFlowVS(fs, channels)

`fs`	A flowSet containing a collection of flow cyometry samples.
`channels`	A character vector identifying the channels/dimensions to be transformed. If any entry in this vector is not present in the flowSet, the function returns with an error.

Let z be a fluorescence channel (column of a flowFrame). We consider transforming z by asinh transformation such that after transformation we obtain the tranformed channel asinh(z/c), where c is a normalizing cofactor.

The estParamFlowVS function estimates cofactors, one for each channel for the entire dataset such that the within-population variance is stabilized in each fluorescence channel. When a fluorescence channel z is transformed by asinh transformation with the optimum cofactor for z, the within-population variances of populations from all samples in the channel z are approximately stabilized.

estParamFlowVS returns a numeric vector representing the optimum cofactors for the requested channels. The optimum cofactor for the input channels[i] is stored in the ith entry of the returned vector.

Ariful Azad

Ariful Azad, Bartek Rajwa, and Alex Pothen (2015), "flowVS: Channel-Specific Variance Stabilization in Flow Cytometry", BMC Bioinformatics, vol 17, pp 1-14, 2016.

transFlowVS

data(HD)
## identify optimum cofactor for CD3 and CD4 channels (from five samples)

cofactors = estParamFlowVS(HD[1:5],channels=c('CD3','CD4'))
# See detail examples in the documentation of the transFlowVS function.