mas4 {xps} | R Documentation |
This function converts a DataTreeSet
into an ExprTreeSet
using the XPS implementation of Affymetrix's MAS 4.0 expression measure.
mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", normalize = FALSE, sc = 500, option = "transcript", exonlevel = "", update = FALSE, xps.scheme = NULL, add.data = TRUE, verbose = TRUE) xpsMAS4(object, ...)
xps.data |
object of class DataTreeSet . |
filename |
file name of ROOT data file. |
filedir |
system directory where ROOT data file should be stored. |
tmpdir |
optional temporary directory where temporary ROOT files should be stored. |
normalize |
logical. If TRUE scale normalization is used after an ExprTreeSet is obtained. |
sc |
value at which all arrays will be scaled to. |
option |
option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only. |
exonlevel |
exon annotation level determining which probes should be used for summarization; exon/genome arrays only. |
update |
logical. If TRUE the existing ROOT data file filename will be updated. |
xps.scheme |
optional alternative SchemeTreeSet . |
add.data |
logical. If TRUE expression data will be included as slot data . |
verbose |
logical, if TRUE print status information. |
object |
object of class DataTreeSet . |
... |
arguments filename ,filedir ,tmpdir ,option ,exonlevel ,xps.scheme . |
This function computes the Affymetrix MAS 4.0 expression measure, i.e. the ‘Average Difference’ expression level, as implemented in XPS.
If normalize=TRUE
then the expression levels will be scaled to sc
.
For sc=0
the expression levels will be scaled to the mean expression level.
xpsMAS4
is the DataTreeSet
method called by function mas4
, however,
expression levels will not be scaled to a common mean expression level.
For further details see mas5
.
An ExprTreeSet
In contrast to function mas4
, expression levels computed with xpsMAS4
will not be scaled to a common mean expression level.
Christian Stratowa
Affymetrix (1999) GeneChip Expression Analysis Algorithm Tutorial, Affymetrix Inc., Santa Clara, CA.
## first, load ROOT scheme file and ROOT data file scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/")) data.mas4 <- mas4(data.test3,"tmp_Test3MAS4",tmpdir="",normalize=TRUE,sc=500, update=TRUE,verbose=FALSE) ## get data.frame expr.mas4 <- validData(data.mas4) head(expr.mas4) ## plot results (negative expression values!) if (interactive()) { boxplot(expr.mas4) } rm(scheme.test3, data.test3) gc()