getAffyProbesetList: Retrieve Affy probeset IDs from DAVID.

In DAVIDQuery: Retrieval from the DAVID bioinformatics data resource into R

Description

For a given Affymetrix microarray chip, retrieve Affy probeset IDs from DAVID. Optionally, a menu is used to pick the chip name.

Usage

getAffyProbesetList(chipname = NULL, menu = TRUE, verbose=FALSE)

Arguments

chipname	Full name or regular expression.
menu	Select chipname from a menu (default=TRUE)
verbose	Print a bit of tracing information along the way (default=FALSE) .

Details

If menu==TRUE, DAVID's table of chip names is retrieved. If chipname is a regular expression, then the menu (if requested) is subsetted accordingly. When the user selects or specifies one of the names, the associated file of probeset names is retrieved, again directly from DAVID, not from Affymetrix.

Value

Character vector of probeset names with 'chipType' attribute containing the chip name.

Note

Use with caution. The returned file is not guaranteed to be correct. In the example above, with the chip "Human Genome U133 Plus 2.0", the list returned includes 40907 probeset IDs on the chip (and no others), but appears to be missing 13768 others.

Author(s)

Roger Day, Alex Lisovich

Examples

head(getAffyProbesetList("Human Genome U133 Plus 2.0", menu=FALSE, verbose=TRUE))
## Not run: 
length(getAffyProbesetList("133|95"))

## End(Not run)

DAVIDQuery documentation built on Sept. 12, 2016, 6:11 a.m.