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  1. In the Genomic Data Sources section of the Edit Study page, for the data you have already added, click Configure Copy Number Data button.
    Info
    titleNote

    This link is available only if you have uploaded copy number data and you are configuring a Copy Number data type (as indicated by the Data Type column on the Edit Study page).

    The Edit Copy Number page, shown in the following figure, opens.
    Edit Copy Number page
  2. Browse for and enter appropriate information to identify and retrieve the copy number mapping file. The fields are described in the following table. An asterisk indicates a required field.

    Field

    Description

    caArray Service Host Name

    Enter the hostname for your local installation or for the CBIIT installation of caArray. If you misspell it, you will receive an error message.

    caArray Experiment ID

    Enter the caArray Experiment ID which you know corresponds with the copy number data.

    Loading Type

    Enter the Loading Type of the data file you plan to map.

    Subject and Sample Mapping File

    Browse for the appropriate CN mapping file. The file must be a CSV file with 3 column format for mapping data files (format: subject id, sample id, file name). Supplemental data uses 6 column-files.

    Bioconductor Service Type

    This is the type of bioconductor module that will be used for segmentation. Select between the two options: DNAcopy or CGHcall.

    call caCGHcall Service URL

    Enter the URL for the grid segmentation service used to access the caCGHcall service. For more information, see caCGHCall CGHcall

    Call Level

    An input parameter to CGHcall. This is the number of discrete values used to represent the copy number level. Select between two options: 3 (consisting of discrete values of -1, 0, 1) or 4 (consisting of discrete values -1, 0, 1, 2)

    caDNACopy Service URL*

    Control for selecting the URL which hosts the caDNACopy grid service. For more information, see DNAcopy

    .

    Change Point Significance Level

    Significance levels for the test to accept change-points

    Early Stopping Criterion

    The sequential boundary used to stop and declare a change

    Permutation Replicates

    The number of permutations used for p-value computation

    Random Number Seed

    The segmentation procedure uses a permutation reference distribution. This should be used if you plan to reproduce the results.

  3. Click Save Segmentation Data Calculation Configuration for a genomic data source. On the screen upload a copy number mapping file and configure the parameters to be sent when computing segmentation data.
    Note
    titleBe Careful

    After a study has been deployed and the genomic source has been loaded, you cannot change these copy number parameters without reloading the data from caArray first.

Remapping Copy Number Data in a Deployed Study

Occasionally you may need to remap copy number data in a deployed study. To do so, follow these steps:

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