Converting {GEOquery} | R Documentation |
Functions to take a GDS data structure from getGEO and coerce it to limma MALists or exprSets.
GDS2MA(GDS,do.log2=FALSE,GPL=NULL) GDS2eSet(GDS,do.log2=FALSE,GPL=NULL)
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 or the
featureData slot of the ExpressionSet instance. |
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.
GDS2MA |
A limma MAList |
GDS2eSet |
An ExpressionSet object |
Sean Davis
See the limma and exprSet help in the appropriate packages
## Not run: gds505 <- getGEO('GDS505') ## Not run: MA <- GDS2MA(gds505) ## Not run: eset <- GDS2eSet(gds505)