[BioC] Question regarding the use of the snapCGH package to analyze aCGH data obtained from TCGA
Ajay Singhal [guest]
guest at bioconductor.org
Wed Aug 6 16:57:44 CEST 2014
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 âTCGA.â 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$design <- (-1). With the previous two commands, rawData was of data type, RGList. Next, I normalized and corrected the background of the data, using the code: MA <- normalizeWithinArrays(backgroundCorrect(rawData, method = "minimum"), method = âmedianâ). This line of code then created an MAList. Next, I set the names for the MAList using the code: names(MA$genes)<-c(âRowâ,"Col","LogRatio","ID","GeneName","Chr","Position","PositionY"). â¨â¨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 = âPositionâ). 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)
attached base packages:
 splines tools parallel stats graphics grDevices
 utils datasets methods base
other attached packages:
 aCGH_1.42.0 multtest_2.20.0 survival_2.37-7
 cluster_1.15.2 GLAD_2.28.1 snapCGH_1.34.0
 ADaCGH2_2.4.0 ff_2.2-13 bit_1.1-12
 cghMCR_1.22.0 CNTools_1.20.0 genefilter_1.46.1
 DNAcopy_1.38.1 BiocInstaller_1.14.2 SMAP_1.28.0
 CGHbase_1.24.0 marray_1.42.0 limma_3.20.8
 Biobase_2.24.0 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
 affy_1.42.3 affyio_1.32.0 annotate_1.42.1
 AnnotationDbi_1.26.0 DBI_0.2-7 fastmatch_1.0-4
 ffbase_0.11.3 GenomeInfoDb_1.0.2 grid_3.1.1
 IRanges_1.22.10 lattice_0.20-29 MASS_7.3-33
 pixmap_0.4-11 preprocessCore_1.26.1 RColorBrewer_1.0-5
 RSQLite_0.11.4 sandwich_2.3-1 stats4_3.1.1
 strucchange_1.5-0 tilingArray_1.42.0 vsn_3.32.0
 waveslim_1.7.3 XML_3.98-1.1 xtable_1.7-3
 zlibbioc_1.10.0 zoo_1.7-11
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