affycomp.table: Expression Assessment Table
In affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

Description Usage Arguments Details Value Author(s) Examples

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

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)

`...`	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?

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.

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

Rafael A. Irizarry

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)