Hi,

I wanted to use the cgh package to run CNV analysis. Essentially I want the regions/genes showing gains and losses. I am using the code provided in the 'cghMCR' package vignette, but I'm not sure if the end result is what it should be. The code is:
#################
##
## Vignette: cghMCR
## Pdf at: http://www.bioconductor.org/packages/bioc/vignettes/cghMCR/inst/doc/findMCR.pdf
##
#################

### Section 4: Identifying Segment Gain Or Loss (SGOL)

library(cghMCR)
library(limma)
library(DNAcopy)
library(CNTools)

require(CNTools, quietly = TRUE)
data("sampleData", package = "CNTools")
head(sampleData)

data(geneInfo)
data(sampleData, package = "CNTools")
set.seed(1234)
convertedData <- getRS(CNSeg(sampleData[which(is.element(sampleData[,
                  "ID"], sample(unique(sampleData[, "ID"]), 20))), ]), by = "gene",
                  imput = FALSE, XY = FALSE, geneMap = geneInfo)

require(cghMCR, quietly = TRUE)
SGOLScores <- SGOL(convertedData, threshold = c(-0.2, 0.2), method = sum)
plot(SGOLScores)

#Based on the SGOL scores, genes in regions of gains or losses can be obtained by a
#set of thresholds, say -20 and 20.

GOIGains <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
                      ]))) > 20), "gains"]
GOILosses <- SGOLScores[which(as.numeric(unlist(gol(SGOLScores[,
                      ]))) < -20), "losses"]
head(gol(GOIGains))
>         gains
169270 0.8809
644147 0.8809
26260  0.8809
157695 0.3416
389607 0.3416
157697 0.3416

------------------------------------------
Shouldn't this return genes that have "gains" > 20 ? Similarly, 'head(gol(GOILosses))' doesn't appear to be giving genes that have a SGOL score < -20.
thanks!
My sessionInfo():
> sessionInfo()
R version 2.10.0 (2009-10-26) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cghMCR_1.4.0         limma_3.2.1          CNTools_1.2.0       
 [4] DNAcopy_1.20.0       int.geneint.db_1.1.1 PAnnBuilder_1.8.0   
 [7] GOstats_2.12.0       graph_1.24.1         Category_2.12.0    
[10] GO.db_2.3.5          multtest_2.2.0       minet_2.0.0         
[13] infotheo_1.1.0       fExtremes_2100.77    fTrading_2100.76    
[16] fGarch_2110.80       fBasics_2100.78      MASS_7.3-3          
[19] timeSeries_2110.87   timeDate_2110.87     R.utils_1.2.4       
[22] R.oo_1.6.5           R.methodsS3_1.0.3    XML_2.6-0           
[25] genefilter_1.28.0    hgu95av2.db_2.3.5    hgu133a.db_2.3.5    
[28] org.Hs.eg.db_2.3.6   RSQLite_0.7-3        DBI_0.2-4           
[31] AnnotationDbi_1.8.0  GEOquery_2.8.0       RCurl_1.2-1         
[34] bitops_1.0-4.1       biomaRt_2.2.0        affy_1.24.1         
[37] Biobase_2.6.0       

loaded via a namespace (and not attached):
[1] affyio_1.14.0        annotate_1.24.0      GSEABase_1.8.0     
[4] preprocessCore_1.8.0 RBGL_1.20.0          splines_2.10.0     
[7] survival_2.35-7      tools_2.10.0         xtable_1.5-6        
> 


      
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