affy (version 1.50.0)

affycompTable: Expression Assessment Table

Description

These functions take as an argument the output of the assessment functions.

Usage

affycompTable(...,Table=NULL,assessment.list=NULL,method.names=NULL)
tableAll(...,assessment.list=NULL,method.names=NULL)
tableDilution(l, method.names=NULL)
tableFC(l, method.names=NULL)
tableFC2(l, method.names=NULL)
tableSignal(l, method.names=NULL)
tableLS(l, method.names=NULL)
tableSpikeInSD(l, method.names=NULL)
tableMA2(l, method.names=NULL)
tableOverallSNR(...,assessment.list=NULL,method.names=NULL,ngenes=12626)
tableRanks(...,assessment.list=NULL,method.names=NULL,ngenes=12626,rank=TRUE)

Arguments

...

lists produced by the assessment functions

Table

If TableAll was used one can send it through this argument

assessment.list

Alternatively, one can also send a list of lists produced by tableAll.

method.names

A character vector with the names of the epxression measure methodology.

l

list of assessments.

rank

if TRUE tableRanks will present ranks instead of local slopes.

ngenes

when computing ranks, out of how many genes should we do it?

Value

• A matrix. One column per each method and one row for each comparison. tableOverallSNR is an exception. Where rows represnt methods.

Details

Read the vignette for more details on what the entries of the table are. affycompTable has a few entries per graph. tableAll has more entries. Once an assessment is used this function knows what to do. You can call any of the assessment functions described in assessSpikeIn, assessDilution, assessSD, assessLS, assessMA2, and assessSpikeInSD.

Note tableRanks and tableOverallSNR work on the results from assessSpikeIn2.

Examples

library(affycompData)
data(rma.assessment) ##this was produced with affycomp.assess
data(mas5.assessment) ##this one too
tmp <- affycompTable(mas5.assessment,rma.assessment)
format(tmp,digit=2)