| dyebias.geo2marray {dyebiasexamples} | R Documentation |
convenience function to convert GEO objects to marray objects
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) |
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.
A full-fledged marrayRaw (if
type was "raw") or marrayNorm (if type was "norm") is returned.
At some point, this functionality should be merged into the convert package.
Philip Lijnzaad
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)
## Not run:
## Running this example takes too much time; if you want that, see the
## second example in the vignette
## End(Not run)