MetaDE.ES: Identify differentially expressed genes by combining effect...

In MetaDE: MetaDE: Microarray meta-analysis for differentially expressed gene detection

Description

Function to fit the meta-analytic fixed- and random-effects models.The data consists of effect sizes and corresponding variances from your own method/calculations.

Usage

MetaDE.ES(x, meta.method = c("FEM", "REM"))

Arguments

x	a list with components. ES: The observed effect sizes. Var: The observed variances corresponding to ES perm.ES: The effect sizes calculated from permutations, perm.ES is NULL if the argument nperm is set as NULL. perm.Var: The corresponding variances calculated from permutations. perm.Var is NULL if the argument nperm is set as NULL.
meta.method	a character string specifying whether a fixed- or a random/mixed-effects model should be fitted. A fixed-effects model is fitted when using meta.method="FEM". Random-effects model is fitted by setting meta.method equal to "REM". See "Details".

Details

The function can be used to combine any of the usual effect size used in meta-analysis,such as standardized mean differences.Simply specify the observed effect sizes via the x\$ES and the corresponding variances vis x\$Var. If the effect sizes and corresponding varicances calculated from permutation are available,then specify them by x\$perm.ES and x\$perm.Var, respectively.

The argument paired is a vecter of logical values to specify whethe the corresponding study is paired design or not. If the study is pair-designed, the effect sizes (corresponding variances) are calcualted using the formula in morris's paper, otherwise calculated using the formulas in choi et al.

In addition, if the components of x, perm.ES and perm.Var, are not "NULL", the p-values are calculated using permutation method, otherwise, the p-values are calculated using parametric method by assupming the z-scores following a standard normal distribution.

Value

The object is a list containing the following components:

zval	test statistics of the aggregated value.
pval	p-values for the test statistics.
FDR	A matrix with one column which has the corrected p-values using Benjamini and Hochberg method (see references).
Qval	test statistics for the test of heterogeneity.
Qpval	p-values for the test of heterogeneity.
tau2	estimated amount of (residual) heterogeneity.

Author(s)

Jia Li and Xingbin Wang

References

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics,2003, i84-i90.

Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B, 57, 289:300.

See Also

ind.cal.ES

Examples

#---example 1: Meta analysis of Differentially expressed genes between two classes----------#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,5))
x<-list(list(exp1,label1),list(exp2,label2))
ind.res<-ind.cal.ES(x,paired=rep(FALSE,2),nperm=100)
MetaDE.ES(ind.res,meta.method='REM')

Example output

Loading required package: survival
Loading required package: impute
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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: combinat

Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn

Loading required package: tools
$mu.hat
 [1] 1.0940742 1.7413051 2.0915977 1.4799549 1.6290456 0.9436879 1.9087713
 [8] 1.0263015 1.9647400 1.5585980 1.1245436 1.5268566 2.3485394 1.3810362
[15] 0.8637464 2.5288764 1.8432231 2.0498139 1.4267858 2.1393629

$mu.var
 [1] 0.4154618 0.7679196 0.3114783 0.2556543 0.2878482 0.2976388 0.2955025
 [8] 0.2299672 1.5763934 0.2637792 0.2322046 0.8105116 0.7570523 0.2477028
[15] 0.3106108 0.3600550 0.3803569 0.3323811 0.2509275 0.3147503

$Qval
 [1] 1.718927271 2.558723504 0.270810787 0.140446579 1.050935022 1.292603317
 [7] 0.597938068 0.632226688 4.578909019 0.462282785 0.101564453 2.866529983
[13] 2.075623100 0.003441046 1.368491278 0.019397695 1.282735586 1.058549495
[19] 0.005512836 0.041738943

$Qpval
 [1] 0.18983119 0.10968712 0.60278841 0.70783746 0.30529184 0.25556875
 [7] 0.43936583 0.42653972 0.03236782 0.49655904 0.74996025 0.09043967
[13] 0.14966881 0.95322258 0.24207127 0.88923236 0.25739102 0.30354624
[19] 0.94081267 0.83811820

$tau2
 [1] 0.35030060 0.94583613 0.00000000 0.00000000 0.02861450 0.13586832
 [7] 0.00000000 0.00000000 2.48095699 0.00000000 0.00000000 1.06393304
[13] 0.80047015 0.00000000 0.16838825 0.00000000 0.17182236 0.03805625
[19] 0.00000000 0.00000000

$zval
 [1] 1.697388 1.987087 3.747695 2.926995 3.036348 1.729751 3.511344 2.140139
 [9] 1.564850 3.034687 2.333678 1.695972 2.699199 2.774850 1.549808 4.214472
[17] 2.988700 3.555464 2.848293 3.813304

$pval
 [1] 5.50e-02 2.65e-02 1.00e-20 1.50e-03 1.50e-03 5.00e-02 1.00e-20 1.55e-02
 [9] 7.55e-02 1.50e-03 9.50e-03 5.55e-02 4.00e-03 2.50e-03 7.95e-02 1.00e-20
[17] 1.50e-03 1.00e-20 2.50e-03 1.00e-20

$FDR
               REM
 [1,] 6.166667e-02
 [2,] 3.533333e-02
 [3,] 4.000000e-20
 [4,] 3.333333e-03
 [5,] 3.333333e-03
 [6,] 6.166667e-02
 [7,] 4.000000e-20
 [8,] 2.214286e-02
 [9,] 7.947368e-02
[10,] 3.333333e-03
[11,] 1.461538e-02
[12,] 6.166667e-02
[13,] 6.666667e-03
[14,] 4.545455e-03
[15,] 7.950000e-02
[16,] 4.000000e-20
[17,] 3.333333e-03
[18,] 4.000000e-20
[19,] 4.545455e-03
[20,] 4.000000e-20

attr(,"nstudy")
[1] 2
attr(,"meta.method")
[1] "REM"
attr(,"class")
[1] "MetaDE.ES"

MetaDE documentation built on May 29, 2017, 9 a.m.