Unlike normal microarrays, which typically include a limited number of spaced, non-overlapping, probes for each known gene, tiling arrays contain many overlapping probes designed to cover large contigs of the genome, or even the whole genome itself. Because of their potential for very high resolution, and coverage, tiling arrays can produce a much more unbiased examination of overall expression of both known and unidentified genes. However, because of the immense number of probes, the .cel files containing the data tend to be very large.
The Basic Tiling Workflow enables you to run a basic workflow for tiling data. The workflow includes options for quality control and ANOVA.
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An Input Data Set. Before you can run the Basic Tiling Workflow, you must import the data into SAS data sets from the raw data files. The Affymetrix Tiling CEL Input Engine can be used to import the data from Affymetrix .cel files into an input SAS data set. The testicular_outdata.sas7bdat data set serves as an example, and is shown below.
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An Experimental Design Data Set (EDDS) for the experiment. The EDDS lists specific information about the design of the experiment. The EDDS is a SAS data set that must be created before the data can be imported. An EDDS is created by the Affymetrix Tiling CEL Input Engine during data import. The edt_condition.sas7bdat EDDS serves as an example, and is shown below.
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A third data set, the Annotation Data Set, is optional. This data set contains information such as gene identity or chromosomal location, for each of the markers.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
When you click , the Basic Tiling Workflow process begins by opening the Workflow Builder. The Workflow Builder builds settings files for each process, containing the information from the data sets and parameters specified in the Basic Tiling Workflow dialog. Once the setting files are generated and saved, the individual processes in the workflow are sequentially opened, populated, and run. The results of the processes are saved in the specified output folder. Finally, a JMP journal is generated, providing links to the workflow dialog and the results of each process.
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Click .
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The Workflow Builder dialog shows the settings for each of the processes in the workflow. You can select and edit individual settings to adjust your analysis.
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Clicking each of the buttons on the journal brings up the output of each of the processes. This enables you to examine each set of output so that adjustments can be made to the individual settings, as needed. For your convenience, links to the default Basic Tiling Workflow processes are given below.
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