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Experiment Management Tutorial

Experiments are groups of samples that should be analyzed together. They are used to store information on statistical test results.

Creating Experiments

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Start by clicking 'New Experiment' on the experiment listing

New experiments must be assigned to an assembly. The experiment name should also be unique to that assembly.

Samples
You can assign samples to the experiment. Samples can only belong to one experiment. Experiments can be used to filter expression views only displaying the assigned samples.

Sample Groups + Factors
You can assign factors to experiment. Factors are based on sample traits. A sample group is displayed for each factor combination. Sample groups will be used to display average sample expression in an upcoming GxSeq version.

Adding Statistical Tests

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Statistical Tests store a Fold Change and Value for each gene in the assembly. An example test is the differential gene expression result generated by DESeq2: http://bioconductor.org/packages/release/bioc/html/DESeq2.html

Statistical Tests are containers for result data. They belong to an experiment and can be created by clicking 'Add Statistical Test' on the experiment edit page.

Tests have an attached Statistic table. This table represents the datafiles containing test results. A datafile must be uploaded to the test by clicking 'Add Statistical Table' on the edit page.

Statistical Tests can store additional datafiles including images, pdfs and text files. These datafiles can be used to display additional results such as PCA analysis or clustering or to attach information such as code history or metrics.

Statistic Tables

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Statistic Tables are uploaded datafiles containing 1 row per gene with columns for Fold-Change and Value. The value can represent any test statistic.

Feature Type
The Feature Type selection is used to denote the kind of annotation you want to lookup. This is often 'Gene' but it may also be 'mRNA' or 'exon' or any other assembly on the feature. The count should be greater than or equal to the number of entries in your file.

ID Key
The ID Key selection is used to choose the feature attribute for text matching. This attribute is generally ID or locus_tag. It may also be 'Name' or 'Gene' depending on how your annotations were generated. Make sure the count of features with this attribute is greater than or equal to the number of entries in your file.

Columns

After selecting a text file from your local system a preview will be displayed including columns selections. You can use this preview to verify column assignment before upload. Columns are assigned by entering the 1-based column index into the form. Changes in the form will be reflected in the preview.

Feature ID
Text column matching the ID attributes in the database. Will be used to lookup features for assignment.

Value
Decimal column of gene statstic values from the test. For example, the adjusted p-value from DESeq2 (padj).

Fold Change
Decimal column of fold change results in statistical test. For example, log2FoldChange in DESeq2.