Question regarding the use of the snapCGH package to analyze aCGH data obtained from TCGA
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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","Positio nY"). ??????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 -- Sent via the guest posting facility at bioconductor.org.
Microarray Annotation CGH snapCGH Microarray Annotation CGH snapCGH • 1.2k views
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@sean-davis-490
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On Wed, Aug 6, 2014 at 10:57 AM, Ajay Singhal [guest] < guest@bioconductor.org> wrote: > 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"). Hi, Ajay. I'm not sure exactly what is giving you the error, but you will probably need to adjust your code a bit to get the chromosome and chromosome location information. An example of how this can be done is available here: http://watson.nci.nih.gov/~sdavis/tutorials/TCGA_data_integration/TCGA .html#cgh-data-preparation So, your "genes" will need to be adjusted slightly. > 

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. > I think the ID="ID" is probably the approach to use. Sean > > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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