pa.calls {panp} | R Documentation |
Function to make gene presence/absence calls based on distance from empirical distribution of chip-specific negative strand matching probesets (NSMP).
pa.calls(object, looseCutoff = 0.02, tightCutoff = 0.01, verbose = FALSE)
object |
an exprSet object (result of running expression-generating function, like expresso(), rma(), mas5(), etc.) Currently, this must be of chip type HGU133A or HGU133 Plus 2.0 |
looseCutoff |
the larger P-value cutoff (see details) |
tightCutoff |
the smaller, more strict P-value cutoff |
verbose |
logical. If 'TRUE' detailed progress messages are reported. |
The function calculates a matrix of P-values for the expression values in the input exprSet. P-values are calculated based on the empirical survivor function (1-CDF) of the set of negative probesets identified by Affymetrix as negative strand matching probesets (NSMP) with no cross hybridization. These probesets are therefore assumed to show nothing but background/machine noise plus some occasional non-specific binding. The P-value returned for any probeset expression value in exprSet is the value of the NSMP survivor function for that expression level.
Presence/Absence calls are derived by applying the two cutoff values to the matrix of P-values for all genes in the exprSet, as follows:
exprSet |
a new exprSet: exprs slot holds Pcalls; se.exprs slot holds Pvals, as follows: |
Pvals |
a matrix of P-values. Each data point is the P-value for the expr at the same x,y coordinates. |
Pcalls |
a matrix of Presence (P), Marginal (M), Absent (A) indicators |
NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. Hence only these two are currently supported by PANP.
Peter Warren
Warren, P., Bienkowska, J., Martini, P., Jackson, J., and Taylor, D., PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays (2005), in preparation
## Load example exprSet data(test133a) ## Generate Pvals and Pcalls matrices from exprSet, using default cutoffs newExprSet <- pa.calls(test133a) ## to access the Pcalls and Pvals: myPcalls <- exprs(newExprSet) myPvals <- se.exprs(newExprSet)