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.
Value
GDS2MA
A limma MAList
GDS2eSet
An ExpressionSet object
Author(s)
Sean Davis
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)