Running examples in ‘DCGL-Ex.R’ failed
The error most likely occurred in:

> ### Name: DCGL-package
> ### Title: Differential Co-expression Analysis and Differential Regulation
> ###   Analysis of Gene Expression Microarray Data
> ### Aliases: DCGL-package DCGL
> ### Keywords: package
> 
> ### ** Examples
> 
> data(exprs) 
> 
> ## divide exprs into two parts corresponding to condition 1 
> ##(exprs.1) and condition 2 (exprs.2) respectively
> expGenes<-rownames(exprs)
> exprs<-exprs[1:100,]
> exprs.1<-exprs[1:100,1:16] 
> exprs.2<-exprs[1:100,17:63]
> 
> DCp.res<-DCp(exprs.1,exprs.2,
+ 	link.method='qth',cutoff=0.25,N=0)
> 
> DCe.res<-DCe(exprs.1,exprs.2,
+ 	link.method='qth',
+ 	cutoff=0.25,
+ 	nbins=10,p=0.1)
> 
> 
> ## combine two Differential Co-expression Analysis results
> DCsum.res<-DCsum(DCp.res,DCe.res,
+ 	DCpcutoff=0.25,DCecutoff=0.4)
> DCsum.res$DCGs[1:3,]
     DCG        dC All.links.DCp DCp.p DCp.q All.links.DCe DC.links DCL.same
1 AGPAT1 0.4988372            35    NA    NA            35       10        7
2 CXCL13 0.6251436            47    NA    NA            47       24       10
3  EP300 0.4838290            40    NA    NA            40       10        7
  DCL.diff DCL.switch        DCe.p        DCe.q
1        2          1 2.665844e-03 6.664610e-02
2       12          2 5.389187e-12 5.389187e-10
3        3          0 7.538507e-03 1.507701e-01
> DCsum.res$DCLs[1:3,]
                Gene.1  Gene.2       cor.1      cor.2        type  cor.diff
AGPAT1; PARN    AGPAT1    PARN 0.709445989 0.08034541 same signed 0.6291006
AGPAT1; CREB3L1 AGPAT1 CREB3L1 0.001836449 0.26709765 same signed 0.2652612
AGPAT1; CHD8    AGPAT1    CHD8 0.764631439 0.10215738 same signed 0.6624741
                   DCG
AGPAT1; PARN    AGPAT1
AGPAT1; CREB3L1 AGPAT1
AGPAT1; CHD8    AGPAT1
> 
> 
> ## sort out differentially regulated genes and differentially regulated links
> data(tf2target) ## TF-to-target relationships
> DRsort.res<-DRsort(DCsum.res$DCGs,DCsum.res$DCLs,tf2target,expGenes)
> ## or
> DRsort.res<-DRsort(DCe.res$DCGs,DCe.res$DCLs,tf2target,expGenes)
> 
> ## plot differentially regulated links
> DRplot.res<-DRplot(DCsum.res$DCGs,DCsum.res$DCLs,
+ 	tf2target,
+ 	expGenes,
+ 	type='TF_bridged_DCL',
+ 	vsize=5,asize=0.25,lcex=0.3,ewidth=1,
+ 	figname=c('TF2target_DCL.pdf','TF_bridged_DCL.pdf'))
The graph of TF_bridged_DCL.pdf has been completed and saved in your working directory.
> 
> 
> ## rank regulators by TED or TDD
> DRrank.res<-DRrank(DCsum.res$DCGs,DCsum.res$DCLs,
+ 	tf2target,
+ 	expGenes,
+ 	rank.method=c('TED','TDD')[1],
+ 	Nperm=0)
> 
> 
> ## rank regulators by RIF\
> data(exprs_design)
> RIF.res<-RIF(exprs,exprs.1,exprs.2,
+ 	tf2target,
+ 	exprs_design,
+ 	p.value=0.05)
Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
Calls: RIF -> lmFit -> getEAWP -> rowMeans
Execution halted