Page History

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• If you have already mapped samples, when you first open this page they are listed in the Samples Mapped to Subjects section. If you have not already mapped samples, all of the samples in the caArray experiment you selected are listed as unmapped, because caIntegrator does not know how these sample names correlate to the patient data in the subject annotation file until you upload the subject to sample mapping file.
• Scroll down the page to see samples that are mapped to the patients in the subject annotation data (). Image ModifiedExample of samples mapped to patients' data AnchorRTF36313131353a204361707469RTF36313131353a204361707469

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Uploading Control Samples

control samples, uploading;study:uploading control samples to;fold change:control samples fileA Control Samples file is used to calculate fold change data, which compares "tumor" sample gene expression in the caArray experiment to the control samples to identify those that exhibit up or down gene regulation. Control samples can be the "normal" samples, but that is not necessarily the case.
To upload the control samples, follow these steps:

• On the Edit Sample Mappings page, click the Map Samples link.
• Click Browse to navigate for the control samples file, and click the Upload Control Samples File button. The control sets display at the top of the page once they have been uploaded (). Image Modified AnchorRTF32393733343a204361707469RTF32393733343a204361707469Example list of control samples

The control samples now display toward the bottom of the page.

• This information will be used when performing other tasks in caIntegrator, to be described in other sections.
• If a Control Set is to be used in Gene Expression For Annotation, or Gene Expression plots for Annotation Query, then the control set should be composed of only samples which are mapped to subjects.

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Configuring Copy Number Data

study:configuring copy number data;copy number:configuring data;genomic data:adding copy number data to;configuring:copy number dataYou can add copy number data for a genomic data source by uploading the mapping file. This allows you to configure parameters to be used when segmentation data is being configured.
The name specified in the third column of the mapping file is specific for each array manufacturer as follows:

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The Edit Copy Number page opens (). Image Modified

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• RTF36353730343a204361707469Edit Copy Number pageBrowse for and enter appropriate information to identify 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. 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.
  caCGHcallcaCGHcall Service URL	Enter the URL for the grid segmentation service used to access the caCGHcall service. For more information, see
  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)
  caDNACopycaDNACopy Service URL*	Control for selecting the URL which hosts the caDNACopy grid service For more information, see
  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.
  Anchor RTF32323739393a205461626c65 RTF32323739393a205461626c65 Fields for retrieving a copy number mapping file.

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• Click Save Segmentation Data Calculation Configuration for a genomic data source. On the screen upload a copy number mapping file (format: subject id, sample id, file name) and configure the parameters to be sent when computing segmentation data.
• 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.

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Remapping Copy Number Data in a Deployed Study*

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

• Select the Manage Studies button and select Edit for the study you wish to remap.
• On the Edit Study page, select Edit under the Genomic Data Sources header.
• Without altering any information, select Save. When the warning box appears, select OK.
• Select ConfigureCopyNumberData.
• Enter the new mapping file in the Subject and Sample Mapping File field. Select Save Segmentation Data Calculation configuration.
• Select Deploy Study.

See also .
AnchorRTF34343437313a204865616469RTF34343437313a204865616469Working 2. hWorking with Imaging Data
study:working with imaging data;imaging data:working withOnce you have loaded subject annotation data and identified patient IDs, you can add either array genomic sample data from caArray which caIntegrator maps by sample IDs to the patient IDs in the subject annotation data, or you can upload image data from NBIA, also mapped by IDs to the subject data. Once you have configured an NBIA image data source for adding images, then you can import image annotation data for the images. Genomic sample data and imaging data are independent of each other, so neither is required before loading the other.
It is essential that you are well acquainted with the data you are working with--the subject annotation data, and the corresponding imaging data in NBIA.
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Adding or Editing Imaging Data Files from NBIA

study:adding imaging data;imaging data:adding to study;adding:imaging data;NBIA:adding files to caIntegrator;editing imaging files;imaging data:editing NBIA images sourcesTo add images from NBIA to the study you are creating, follow these steps:

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The imaging data displays on the Edit Study page under the Imaging Data Sources section (). Image Modified

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• RTF36363438313a204361707469Imaging Data Sources section of the Edit Study page.Once the data is uploaded, you can add image annotations. For more information, see .

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Adding or Editing Image Annotations

adding:image annotations;images:adding annotations;annotation:image, editing;editing:image annotationsAfter you have configured an image After you have configured an image data source with an NBIA Grid service and uploaded the image data, described in , you can load image annotations into caIntegrator from a file in CSV format or through an Annotations and Image Markup (AIM) service.

• The image data shown in the Imaging Data Sources section indicate whether or not annotations have already be imported from a file for these sources. See marked area in .

Image Modified

• Imaging Data Sources section of the Edit Study page. The circled section in this screen shot indicates that annotations have been uploaded for this image collection.

To add image annotations from a file, follow these steps:

• On the Edit Study page, click the Edit Annotations button under the Image Data Sources section.
• If you have not yet imported annotations, clicking this button opens the page from which you can import image annotations (). Continue with the steps in this section. If you are editing annotations, clicking this button opens the Define Fields for Image Annotations dialog box where you can edit annotations. See . Image Removed AnchorRTF31373936333a204361707469RTF31373936333a204361707469Page for adding imaging data annotations
  Image Added
• Select the radio button Upload Annotation File.
• Click Browse to select an annotation CSV file for upload.
• An image annotation CSV file must include an Image Series ID column. See the highlighted column in . Image Modified AnchorRTF38393630333a204361707469RTF38393630333a204361707469Image annotations file
• Check the box for Create a new Annotation Definition if one is not found (if appropriate).
• Click Add.

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Once you have created external links for a study, when the study is open, an External Links section showing the link(s) displays on the left sidebar of the page (). Image Modified

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Click the link to open a page that displays appropriately formatted web page links (). Image Modified

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Deploying the Study

study:deployingWhen When you are ready to deploy the study, click the Deploy Study button on the Edit Study page. caIntegrator retrieves the selected data from the data service(s) you defined and makes the study available to a study manager or to anyone else who may want to analyze the study's data. Using the Manage Studies feature, you can then configure and share data queries and data lists with all investigators who access the study.
Note that you can continue to work in caIntegrator while study is being deployed. See also .
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Managing a Study

• A user without management privileges has no access to this section of caIntegrator.

study:managing;managing:study;study:editing;editing:studyOnce Once you have started to create a study or have deployed it, you can update an existing study in the following ways:

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• On the left sidebar, click Manage Studies. The Manage Studies page appears (). Image Modified AnchorRTF35303837323a204361707469RTF35303837323a204361707469Manage Studies page

All of the "in process" or "completed" studies display on this page, with associated metadata. Note that whoever edited or updated the study last is shown in the Last Modified Column, indicated as the Study Manager.

• Click the Edit link corresponding to your study of choice to open the Edit Studies page (). Image Modified AnchorRTF37303334343a204361707469RTF37303334343a204361707469Edit Studies page where you can edit any details for an existing study

On this page you can edit any details such as adding or deleting files, survival values, and so forth. For information about working with the Edit Study feature, see .

• Click the Delete link to delete the corresponding study.

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• .

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Managing Platforms

managing:platforms;platforms, managingcaIntegrator Integrator supports a limited number of array platforms, all of which originate from Agilent or Affymetrix. While they do not represent all of the platforms supported by caArray, caIntegrator must have array definitions loaded for the platforms it supports, and be able to properly load the data from caArray and parse it.
You can create a study without genomic data, but you cannot add genomic data to a caIntegrator study without a corresponding supported array platform. If you add more than one set of genomic data to the study, you can specify more than one platform for the study.
On the Manage Platforms page, you can identify, add or remove supported platforms.
To manage platforms in caIntegrator, follow these steps:

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The Manage Platforms page that opens lists the platforms caIntegrator currently supports, those that the system can pull from caArray (). You can also add a new platform by entering information in the fields in the Create a New Platform section. Image Modified

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• To add a platform, in the Platform Type field, select the appropriate platform type from the drop down list.
• Click Browse to navigate for the Affymetrix or Agilent file you want to add.
• Tab-delimited .txt or .tsv Agilent platform annotation files must contain the following column headers: ProbeId, GeneSymbol, GeneName and Accessions.
• Enter a Platform Name if the file is a NON-GEML.xml file.

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• Click the Browse button to browse for the appropriate annotation file. When you have located it, click Open in the Upload File dialog box. The system displays the annotation file you select in the Annotation File box.
• Once all parameters have been entered, click Create Platform.

platform, deployingThe The platform deployment can be time-consuming. If the platform takes more than 12 hours to deploy, caIntegrator displays a "timed out" message. At that point, you can delete the platform, even if it has not loaded to the system.

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