| mas5 {xps} | R Documentation |
This function converts a DataTreeSet into an ExprTreeSet
using the XPS implementation of Affymetrix's MAS 5.0 expression measure.
mas5(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)
xpsMAS5(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 5.0 expression measure as implemented in XPS.
Although this implementation is based on the Affymetrix ‘sadd_whitepaper.pdf’, it
can be used to compute an expression level for both expression arrays and exon arrays.
For exon arrays it is necessary to supply the requested option and exonlevel.
Following options are valid for exon arrays:
transcript: | expression levels are computed for transcript clusters, i.e. probe sets containing the same ‘transcript_cluster_id’. |
exon: | expression levels are computed for exon clusters, i.e. probe sets containing the same ‘exon_id’, where each exon cluster consists of one or more probesets. |
probeset: | expression levels are computed for individual probe sets, i.e. for each ‘probeset_id’. |
Following exonlevel annotations are valid for exon arrays:
core: | probesets supported by RefSeq and full-length GenBank transcripts. | |
metacore: | core meta-probesets. | |
extended: | probesets with other cDNA support. | |
metaextended: | extended meta-probesets. | |
full: | probesets supported by gene predictions only. | |
metafull: | full meta-probesets. | |
ambiguous: | ambiguous probesets only. | |
affx: | standard AFFX controls. | |
all: | combination of above (including affx). |
Following exonlevel annotations are valid for whole genome arrays:
core: | probesets with category ‘unique’, ‘similar’ and ‘mixed’. | |
metacore: | probesets with category ‘unique’ only. | |
affx: | standard AFFX controls. | |
all: | combination of above (including affx). |
Exon levels can also be combined, with following combinations being most useful:
exonlevel="metacore+affx": | core meta-probesets plus AFFX controls |
exonlevel="core+extended": | probesets with cDNA support |
exonlevel="core+extended+full": | supported plus predicted probesets |
Exon level annotations are described in the Affymetrix whitepaper ‘exon_probeset_trans_clust_whitepaper.pdf’.
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.
If update=TRUE then the existing ROOT file filename will be
updated, however, this is usually only recommended as option for function express.
In order to use an alternative SchemeTreeSet set the corresponding SchemeTreeSet
xps.scheme.
xpsMAS5 is the DataTreeSet method called by function mas5, however,
expression levels will not be scaled to a common mean expression level.
An ExprTreeSet
In contrast to function mas5, expression levels computed with xpsMAS5
will not be scaled to a common mean expression level.
Christian Stratowa
Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf
Affymetrix (2005) Exon Probeset Annotations and Transcript Cluster Groupings, Affymetrix Inc., Santa Clara, CA, exon_probeset_trans_clust_whitepaper.pdf.
## 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.mas5 <- mas5(data.test3,"tmp_Test3MAS5",tmpdir="",normalize=TRUE,sc=500,update=TRUE,verbose=FALSE)
## get data.frame
expr.mas5 <- validData(data.mas5)
head(expr.mas5)
## plot results
if (interactive()) {
boxplot(data.mas5)
boxplot(log2(expr.mas5))
}
rm(scheme.test3, data.test3)
gc()