proboscis {MAQCsubset} | R Documentation

## Produce a plot similar to Figure 2 of the Shippy MAQC paper (PMID 16964226).

### Description

Produce a plot similar to Figure 2 of the Shippy MAQC paper (PMID 16964226).

### Usage

    proboscis(es, site=1, ABp=0.001, CDp=0.01, mmrad=100)

### Arguments

`es` | `ExpressionSet` instance with MAQC assay results
`site` | numeric code – site to be assessed
`ABp` | ABp – p-value threshold to declare concentration of gene in sample A to be different from ehe concentration in sample B
`CDp` | CDp – p-value threshold to declare concentration of gene in sample C to be different from the concentration in sample D
`mmrad` | numeric radius of the moving mean used to smooth the proportions differentially expressed

### Details

Figure 2 of the Shippy paper consists of a collection of plots of estimated probabilities of self-consistent monotone titration – briefly, samples are such that A has 100% USRNA, B has 100% Ambion brain, C has 75% USRNA+25% brain, D has 25% USRNA, 75% brain. Self-consistent monotone titration holds for gene g if microarray measures for that gene satisfy A > C > D > B or B > C > D > A. The estimated probability functions look like a creature sticking its nose over a wall, thus the name of this function.

### Value

an instance of `proboStruct`, for which a plot and lines method are available.

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### References

PMID 16964226

### Examples

    data(afxsubRMAES)
    NN2 = proboscis(afxsubRMAES, site=2)
    plot(NN2)

[Package MAQCsubset version 1.0.14 Index]