[BioC] Question regarding the use of the snapCGH package to analyze aCGH data obtained from TCGA

[Ajay Singhal [guest]]

I am currently working on the analysis of array CGH data of Glioblastoma multiforme patients, obtained from the TCGA website. The data was obtained from the Level 1 archive of CNV (CN Array) data type from the Agilent Human Genome CGH Microarray 244A platform.

Initially, I created an object called arrayFiles by specifying the path name for the TCGA data and the pattern set to “TCGA.” Next, I read the raw data into R using the function, read.maImages, using the following code: rawData <- read.maimages(arrayFiles, source = "agilent", columns =list(R = "rMedianSignal", G = "gMedianSignal", Rb = "rBGMedianSignal",Gb = "gBGMedianSignal"), annotation = c("Row", "Col", "LogRatio", "ProbeName","GeneName", "SystematicName", "PositionX", "PositionY"), names = basename(arrayFiles)). 

I set the design for the rawData, using the following code: rawData$design <- (-1). With the previous two commands, rawData was of data type, RGList. Next, I normalized and corrected the background of the data, using the code: MA <- normalizeWithinArrays(backgroundCorrect(rawData, method = "minimum"), method = “median”). This line of code then created an MAList. Next, I set the names for the MAList using the code: names(MA$genes)<-c(“Row”,"Col","LogRatio","ID","GeneName","Chr","Position","PositionY"). 

Next, the processCGH function from the snapCGH package was implemented on the MA object, using the code: MA2 <- processCGH(MA,method.of.averaging=mean, ID = “Position”). However, this command gave the error message: Error in segList$genes : object of type 'closure' is not subsettable. 

Additionally, when I had run the same commands previously, a different error showed up: Error in processCGH(MA, method.of.averaging = mean, ID = "ID") : object 'segList' not found. 

What would be a good way to fix these errors? I really appreciate any help with this issue. Thank you so much for your time.

 -- output of sessionInfo(): 

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] splines   tools     parallel  stats     graphics  grDevices
 [7] utils     datasets  methods   base     

other attached packages:
 [1] aCGH_1.42.0          multtest_2.20.0      survival_2.37-7     
 [4] cluster_1.15.2       GLAD_2.28.1          snapCGH_1.34.0      
 [7] ADaCGH2_2.4.0        ff_2.2-13            bit_1.1-12          
[10] cghMCR_1.22.0        CNTools_1.20.0       genefilter_1.46.1   
[13] DNAcopy_1.38.1       BiocInstaller_1.14.2 SMAP_1.28.0         
[16] CGHbase_1.24.0       marray_1.42.0        limma_3.20.8        
[19] Biobase_2.24.0       BiocGenerics_0.10.0 

loaded via a namespace (and not attached):
 [1] affy_1.42.3           affyio_1.32.0         annotate_1.42.1      
 [4] AnnotationDbi_1.26.0  DBI_0.2-7             fastmatch_1.0-4      
 [7] ffbase_0.11.3         GenomeInfoDb_1.0.2    grid_3.1.1           
[10] IRanges_1.22.10       lattice_0.20-29       MASS_7.3-33          
[13] pixmap_0.4-11         preprocessCore_1.26.1 RColorBrewer_1.0-5   
[16] RSQLite_0.11.4        sandwich_2.3-1        stats4_3.1.1         
[19] strucchange_1.5-0     tilingArray_1.42.0    vsn_3.32.0           
[22] waveslim_1.7.3        XML_3.98-1.1          xtable_1.7-3         
[25] zlibbioc_1.10.0       zoo_1.7-11

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