dyebias.geo2marray {dyebiasexamples} | R Documentation

## convenience function to convert GEO objects to marray objects

### Description

convenience function to convert GEO objects to marray objects

### Arguments

`gse` | GSE data set
`slide.ids` | Return only the slides with these ids. If NULL, return all.
`type` | what to extract; must be either "norm" or "raw".
`gene.selector` | function(table) acting on Table(GPL) giving back an index with the rows considered to be genes.
`reporterid.name` | column containing the reporter.id, in Table(gpl).
`cy3.name` | The column name containing the factor value for the Cy3 (green) channel
`cy5.name` | The column name containing the factor value for the Cy5 (red) channel
`R.name` | column name for extracting the R data from Table(gsm)
`G.name` | column name for extracting the G data from Table(gsm)
`M.name` | column name for extracting the M data from Table(gsm)
`A.name` | column name for extracting the A data from Table(gsm)
`Rf.name` | column name for extracting the Rf data from Table(gsm)
`Gf.name` | column name for extracting the Gf data from Table(gsm)
`Rb.name` | column name for extracting the Rb data from Table(gsm)
`Gb.name` | column name for extracting the Gb data from Table(gsm)

### Details

The `XYZ.name` mechanism is the same as that used in `read.marrayRaw`; i.e. you specify the name of the column that contains the desired data.

### Value

A full-fledged marrayRaw (if `type` was "raw") or marrayNorm (if `type` was "norm") is returned.

### Note

At some point, this functionality should be merged into the convert package.

### Author(s)

Philip Lijnzaad

### References

Davis, S. and Meltzer, P.S (2007). GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23, 1846–1847 (doi:10.1093/bioinformatics/btm254).

Dudoit, S. and Yang, Y.H. (2002) Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In: Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger, S.L. (eds.) The Analysis of Gene Expression Data: Methods and Software, New~York: Springer

Chen,S., de~Vries, M.A. and Bell, S.P. (2007) Genes Dev. 21, 2897–2907 "Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading" (doi:10.1101/gad.1596807)

### Examples

    ## Not run:
      ## Running this example takes too much time; if you want that, see the
      ## second example in the vignette
    ## End(Not run)

[Package dyebiasexamples version 1.0.3 Index]