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 â€œTCGA.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$design
> <- (-1). With the previous two commands, rawData was of data type, RGList.
> Next, I normalized and corrected the background of the data, using the
> code: MA <- normalizeWithinArrays(backgroundCorrect(rawData, method =
> "minimum"), method = â€œmedianâ€ ). This line of code then created an
> MAList. Next, I set the names for the MAList using the code:
> names(MA$genes)<-c(â€œRowâ€
> ,"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.


> 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 = â€œPositionâ€ ). 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.
>
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