getUniqueLL {affycoretools} | R Documentation |
This function will take a vector of Affy IDs and return a vector of Entrez IDs that have replicated IDs removed. The resulting vector will still have the corresponding Affy IDs appended as names, which is important for some functions.
getUniqueLL(probes, annot)
probes |
A vector of probe IDs |
annot |
The annotation package for the chip used |
Subsetting a set of Affy IDs to unique Entrez Gene IDs is a common
thing to do prior to doing a hypergeometric test. Functions such as
hyperGtest
can use un-named vectors of Entrez
IDs (e.g., unique(getLL(probeIDs, annot))), but there is some
functionality that requires the Entrez Gene IDs to be in a named
vector, with the names being the associated Probeset IDs.
As an example, hyperGoutput
will only work correctly if the
input Entrez ID vector is named with the associated Probeset IDs.
A named vector of unique Entrez IDs
James W. MacDonald <jmacdon@med.umich.edu>