Converting {GEOquery}R Documentation

Convert a GDS datastructure to a BioConductor datastructure

Description

Functions to take a GDS data structure from getGEO and coerce it to limma MALists or exprSets.

Usage

GDS2MA(GDS,do.log2=FALSE,GPL=NULL)
GDS2eSet(GDS,do.log2=FALSE)

Arguments

GDS The GDS datastructure returned by getGEO
do.log2 Boolean, should the data in the GDS be log2 transformed before inserting into the new data structure
GPL Either a GPL data structure (from a call to getGEO) or NULL. If NULL, this will cause a call to getGEO to produce a GPL. The gene information from the GPL is then used to construct the genes slot of the resulting limma MAList object.

Details

This function just rearranges one data structure into another. For GDS, it also deals appropriately with making the "targets" list item for the limma data structure and the phenoData slot of exprSets.

Value

GDS2MA A limma MAList
GDS2eSet A exprSet object

Author(s)

Sean Davis

References

See the limma and exprSet help in the appropriate packages

Examples


## Not run: gds505 <- getGEO('GDS505')
## Not run: MA <- GDS2MA(gds505)
## Not run: eset <- GDS2eSet(gds505)


[Package GEOquery version 1.7.2 Index]