DownloadLandData AllGenes.pdf

From Array Suite Wiki

Download Land Data To Local Analysis

The function allows users to retrieve data for all genes for a list of samples,as OmicData/Table to a Local Analysis project.

20130826 LandTools1.png

Data Types

The available data types for download depend on the availability in the Land; descriptions for the data types can be found here.

Tips.pngFor RNA-seq expression data, RnaSeq_Transcript is the proper data mode, not GeneBas

.

Options

  • Land: the land data to query input genes
  • Project: the target ArrayStudio project to store downloaded Land data
  • Choose one or more data type to download: choose the land data type to download, each one will be a OmicData/Table in ArrayStudio project
  • Data format
    • Original data: the original data values as stored in Land, such as RNA-Seq FRKM at transcript level and microarray data at probeset level.
    • Gene level data: data values are summarized at gene level
    • Matrix data: data values are organized as feature * Samples in "microarray" format
    • Full meta data: the full sample meta data will be downloaded as a table in the project. By default, only PrimaryGrouping and SecondaryGrouping columns are attached as design in each generated OmicData.
    • Counts instead of FPKM: If retrieving RNAseq data, will return raw read counts for each gene, instead of FPKM values. Use this if you wish to perform DEseq or Voom analysis, or another analysis expecting raw count data.
  • Input samples: a list of samples to query. Samples can also be loaded from Manage SampleSet in ArrayLand
  • Output name: name prefix for download data objects

Output

Downloaded data will be listed in the targeted project. These omic data will be saved as in-file rather than in-memory. If majority of the data matrix are zeros, such as feature * sample matrix for fusion, mutation and junction, the Omic data will be saved as sparse matrix data. These improvements significantly reduce memory usage by sacrificing little performance (data loading speed).

Here is one screenshot:

20130826 LandTools2.png