mas5.call {xps} | R Documentation

## MAS 5.0 Absolute Detection Call

### Description

Performs the Wilcoxon signed rank-based gene expression presence/absence detection algorithm first implemented in the Affymetrix Microarray Suite version 5.

### Usage

    mas5.call(xps.data,
              filename = character(0), filedir = getwd(), tmpdir = "",
              tau = 0.015, alpha1 = 0.04, alpha2 = 0.06, ignore.saturated = TRUE,
              option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

    xpsMAS5Call(object, ...)

### Arguments

`xps.data` | object of class `DataTreeSet`.
`filename` | file name of ROOT data file.
`filedir` | system directory where ROOT data file should be stored.
`tmpdir` | optional temporary directory where temporary ROOT files should be stored.
`tau` | a small positive constant.
`alpha1` | a significance threshold in (0,alpha2).
`alpha2` | a significance threshold in (alpha1,0.5).
`ignore.saturated` | logical. If `TRUE` do the saturation correction described in the paper, with a saturation level of 46000.
`option` | option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
`exonlevel` | exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
`xps.scheme` | optional alternative `SchemeTreeSet`.
`add.data` | logical. If `TRUE` call data will be added to slots `data` and `detcall`.
`verbose` | logical, if `TRUE` print status information.
`object` | object of class `DataTreeSet`.
`...` | the arguments described above.

### Details

This function performs the hypothesis test:

H0: median(Ri) = tau, corresponding to absence of transcript H1: median(Ri) > tau, corresponding to presence of transcript

where Ri = (PMi - MMi) / (PMi + MMi) for each i a probe-pair in the probe-set represented by data.

The p-value that is returned estimates the usual quantity:

Pr(observing a more "present looking" probe-set than data | data is absent)

Small p-values imply presence while large ones imply absence of transcript. The detection call is computed by thresholding the p-value as in:

call “P” if p-value < alpha1
call “M” if alpha1 <= p-value < alpha2
call “A” if alpha2 <= p-value

The defaults for `tau`, `alpha1` and `alpha2` correspond to those in MAS5.0 for expression arrays. However, when using this function for exon or whole genome arrays, new values for `alpha1` and `alpha2` must be determined. The recommended function for exon/genome arrays is `dabg.call`.

In order to use an alternative `SchemeTreeSet` set the corresponding SchemeTreeSet `xps.scheme`.

`xpsMAS5Call` is the `DataTreeSet` method called by function `mas5.call`, containing the same parameters.

### Value

A `CallTreeSet`

### Author(s)

Christian Stratowa

### References

Liu, W. M. and Mei, R. and Di, X. and Ryder, T. B. and Hubbell, E. and Dee, S. and Webster, T. A. and Harrington, C. A. and Ho, M. H. and Baid, J. and Smeekens, S. P. (2002) Analysis of high density expression microarrays with signed-rank call algorithms, Bioinformatics, 18(12), pp. 1593-1599.

Liu, W. and Mei, R. and Bartell, D. M. and Di, X. and Webster, T. A. and Ryder, T. (2001) Rank-based algorithms for analysis of microarrays, Proceedings of SPIE, Microarrays: Optical Technologies and Informatics, 4266.

Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

### See Also

`dabg.call`

### Examples

    ## first, load ROOT scheme file and ROOT data file
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

    ## MAS5 detection call
    call.mas5 <- mas5.call(data.test3,"tmp_Test3Call",tmpdir="",verbose=FALSE)

    ## get data.frames
    pval.mas5 <- pvalData(call.mas5)
    pres.mas5 <- presCall(call.mas5)
    head(pval.mas5)
    head(pres.mas5)

    ## plot results
    if (interactive()) {
    callplot(call.mas5, beside=FALSE, ylim=c(0,125))
    }

    rm(scheme.test3, data.test3)
    gc()

[Package xps version 1.4.10 Index]