Functions to take a GDS data structure from getGEO and coerce it to
limma MALists or ExpressionSets.
GDS2MA(GDS,do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE,getGPL=TRUE)
GDS2eSet(GDS,do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE,getGPL=TRUE)
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 or the
featureData
slot of the ExpressionSet
instance.
- AnnotGPL
- In general, the annotation GPL files will be available
for GDS records, so the default is to use these files over the
user-submitted GPL files
- getGPL
- A boolean defaulting to TRUE as to whether or not to
download and include GPL information when converting to
ExpressionSet or MAList.
You may want to set this to FALSE if you know that you are going to
annotate your featureData using Bioconductor tools rather than relying
on information provided through NCBI GEO. Download times can also
be greatly reduced by specifying FALSE.
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 ExpressionSets.
References
See the limma and ExpressionSet help in the appropriate packages
Examples
## Not run: gds505 <- getGEO('GDS505')
## Not run: MA <- GDS2MA(gds505)
## Not run: eset <- GDS2eSet(gds505)