Manage Land Sample Metadata

From Array Suite Wiki

Jump to: navigation, search

Contents

Manage Land Sample Metadata

Overview

Users with sufficient Land privileges can manage columns of metadata for samples. For example, additional samples can be added, updated, or removed.

To access this function, click Manage | Samples | Manage Sample Metadata:

Land ManageLandSampleMetadata Menu.png

Options

Land ManageLandSampleMetadata Window.png

Add/Replace Sample Metadata

Metadata for samples can be added to a Land before or after sample data [such as [ALV]]/[[TLV] for ArrayLands] files have been published. Only samples included in Sample Metadata will be displayed in the Sample Distribution View. Furthermore, sample data (e.g. expression or mutation data for a gene) will not be visible in gene-level Views unless Sample metadata have been added.

We have found that when building GeneticsLands, it is best practice to register metadata to the Land before adding genetic data into the Land. This practice avoids conflicting sample IDs and ensures access controls are in-place before restricted genetic data are added. For GeneticsLands only, the ProjectName variable is required to be included and non-missing for all samples in the file being imported to ensure the project-level access controls are appropriate. An empty string or "." will be considered missing, anything else will be read as the ProjectName value. This restriction applies to both new and existing samples.

Warning.png WARNING: Please see This page for restrictions on metadata column names.


To add or update Sample metadata, click Add/Replace:

Land AddReplaceSampleMetadata Window.png

A table with Sample IDs in the first column and additional metadata columns can be added in the following ways:

  • tab-delimited file: A text table, with data in a row separated by tabs
  • .osobj file: An OmicSoft Table object from an Analysis project, saved as an osobj file.
  • local analysis: An OmicSoft Table object from an Analysis project.
  • triplets: A tab-delimited file for sparse data, where column 1 is sample ID, column 2 is variable name, and column 3 is the value. See an example here.

Only samples included in the table will be added or updated. By default, existing metadata columns will not be removed, even if they are excluded from the table.

  • Clear existing attributes for existing samples: This option will apply to samples that already exist in the metadata table. If updating the metadata with a new table that is missing columns which are currently in Land, the data in these columns will be cleared from the original metadata table.

During import, metadata columns can also be grouped into multi-level categories:

Land SampleMetadata Tree.png

[back to top]


Add Variable Meta Data

Clear Selected

To clear metadata for samples, first select those samples in the table, then click Clear Selected. When the following warning pops up:

Land ClearSampleMetadata Window.png

click Yes. The metadata for selected samples will be removed.

[back to top]

Related Articles

[back to top]

EnvelopeLarge2.png