background
character string used to indicate what
background gene list should be used in Fisher's exact
test for overrepresentation. The default value is
"data.set"
which indicates that the gene list of
the input pSI data set will be used to represent the
background gene list. This would be used in the case when
the input pSI data set is comprised of genes derived from
the same species as the genes found in the candidate gene
list. background
can take on two other values, the
first of which is "human.mouse"
.
"human.mouse"
indicates that the background gene
list will be comprised of intersection of two lists: 1)
all genes in the input pSI dataset (all are human genes),
2) all genes with clear human-mouse homologs. This option
would be used in the case when the input data set is
comprised of human genes (i.e. genes from a human
microarray) and the candidate gene list being tested is
comprised of mouse genes. The last value
background
can take on is "mouse.human"
.
"mouse.human"
indicates that the background gene
list will be comprised of intersection of two lists: 1)
all genes in the input pSI dataset (all are mouse genes),
2) all genes with clear mouse-human homologs. This option
would be used in the case when the input data set is
comprised of mouse genes (i.e. genes from a mouse
microarray) and the candidate gene list being tested is
comprised of human genes.