Numeric. Fraction of differentially expressed genes.
up
Numeric. Fraction of up-regulated genes among the
differentially expressed genes.
nrstrata
Numeric. Number of probe strata.
miss
Numeric. Fraction of data points that is randomly sampled
and set to NA.
log2scale
Logical. If TRUE, glog on base 2 is used, if FALSE,
(the default), then base e.
h1
Matrix. Calibrated and transformed data, according, e.g., to
vsn
sim
List. The output of a previous call to
sagmbSimulateData, see Value
Details
Please see the vignette.
Value
For sagmbSimulateData, a list with four components:
hy, an n x d matrix with the true (=simulated)
calibrated, transformed data;
y, an n x d matrix with the simulated
uncalibrated raw data - this is intended to be fed into
vsn;
is.de, a logical vector of length n, specifying
which probes are simulated to be differentially expressed.
strata, a factor of length n.
For sagmbSimulateData, a number: the root mean squared
difference between true and estimated transformed data.
Author(s)
Wolfgang Huber
References
Wolfgang Huber, Anja von Heydebreck, Holger Sueltmann,
Annemarie Poustka, and Martin Vingron (2003)
"Parameter estimation for the calibration and variance stabilization
of microarray data",
Statistical Applications in Genetics and Molecular Biology:
Vol. 2: No. 1, Article 3.
http://www.bepress.com/sagmb/vol2/iss1/art3
See Also
vsn
Examples
sim <- sagmbSimulateData(nrstrata=4)
ny <- vsn(sim$y, strata=sim$strata)
res <- sagmbAssess(exprs(ny), sim)
res
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(vsn)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/vsn/sagmbSimulateData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sagmbSimulateData
> ### Title: Simulate data and assess vsn's parameter estimation
> ### Aliases: sagmbSimulateData sagmbAssess
> ### Keywords: datagen
>
> ### ** Examples
>
> sim <- sagmbSimulateData(nrstrata=4)
> ny <- vsn(sim$y, strata=sim$strata)
Note:
The function 'vsn' has been superseded by 'vsn2'.
The function 'vsn' remains in the package for backward compatibility,
but for new projects, please use 'vsn2'.
> res <- sagmbAssess(exprs(ny), sim)
> res
[1] 0.01501352
>
>
>
>
>
> dev.off()
null device
1
>