exprReslt-class {mmgmos} | R Documentation |
This is a class representation for Affymetrix GeneChip probe level data.
The main component are the intensities, estimated expression levels and the confidence
of expression levels from multiple arrays
of the same CDF
type. In extends exprSet-class
.
Objects can be created by calls of the form new("exprReslt", ...)
.
prcfive
:prctwfive
:prcfifty
:prcsevfive
:prcninfive
:exprs
:se.exprs
:phenoData
:exprSet
.description
:characterOrMIAME
has been
defined just for this.annotation
:exprSet
instance.notes
:
Class "exprSet"
, directly.
signature(object = "exprReslt")
: obtains the 50 percentile of the estimated
expression levels. signature(object = "exprReslt")
: replaces the 50 percentile of the estimated
expression levels. signature(object = "exprReslt")
: obtains the 5 percentile of the estimated
expression levels. signature(object = "exprReslt")
: replaces the 5 percentile of the estimated
expression levels. signature(object = "exprReslt")
: obtains the 95 percentile of the estimated
expression levels. signature(object = "exprReslt")
: replaces the 95 percentile of the estimated
expression levels. signature(object = "exprReslt")
: obtains the 75 percentile of the estimated
expression levels. signature(object = "exprReslt")
: replaces the 75 percentile of the estimated
expression levels. signature(object = "exprReslt")
: obtains the 25 percentile of the estimated
expression levels. signature(object = "exprReslt")
: replaces the 25 percentile of the estimated
expression levels. signature(object = "exprReslt")
: renders information about the exprReslt in a concise
way on stdout. signature(x = "exprReslt")
: writes the expression levels and related confidences to
files. It takes the same arguments as write.table
. The argument "file" does not need to set any
extension. The different file marks and extension "csv" will be added automatically. The default file name is "tmp".
In the final results, expression levels are in the file "tmp_exprs.csv", standard deviations in
"tmp_se.csv", 5 percentiles in "tmp_prctile5.csv", likewise, 25, 50, 75 and 95 percentiles in "tmp_prctile25.csv",
"tmp_prctile50.csv", "tmp_prctile75.csv" and "tmp_prctile95.csv" respectively. This class is better described in the vignette.
Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence
Related method mmgmos
and related class exprSet-class
.
## load example data from package Affy data(affybatch.example) ## use method mmgmos to calculate the expressiong levels and related confidences ## of the measures for affybatch.example eset<-mmgmos(affybatch.example) ## save the expression resluts into files write.reslts(eset, file="example")