caArray002

Topic: caArray Usage

Release: caArray 2.0 and above

Date entered: 01/06/2009

Question

How to Upload MicroArray Gene Expression Data into caArray?

I want to load data related to a microarray gene expression experiment into caArray. Where should each piece of data go in caArray?

Answer

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A microarray gene expression experiment is typically associated with the following types of files: array design files, sample annotation files, and raw and/or processed data files. In addition, a user might also want to associate with a particular experiment files that describe the experiment, files that describe the samples, and other misc. files.

caArray allows a user to load all types of files into the system. Furthermore, caArray will perform data parsing for some of those files if it has the corresponding data parsing modules installed. The caArray User Guide has detailed descriptions on the types of files supported by caArray and steps taken to upload, validate, and import those files. Given that in most cases a user uploads data generated from a particular array platform at a time, this document provides step-wise description on the data upload/validate/import process in caArray for each supported array platform.

Step 1. (for all array platforms): Check the availability of Array Design File(s).

Before an experiment is created in caArray, the user should first check whether the corresponding Array Design File(s) already exist in caArray by clicking the "Manage Array Designs" link under the "Curation" section of the caArray left navigation panel, as shown in the image below.

!Manage-Arrary-Design.jpg_!

If the corresponding Array Design File(s) for the array platform used in the experiment are found, the user can proceed to Step 2.

!Upload-Arrary-Design.jpg_!

Otherwise, the user should click the "import a New Array Design" link as shown in Figure 2 and follow the process described in Figure 3 to import an Array Design File (only a registered user can import an Array Design File).

!Import-Array-Design.jpg_!

Please note that any other array design format not mentioned in Figure 3 is not supported by caArray up to version 2.1.1

h5}}Step 2 (for all array platforms): Create an experiment{{h5End

The caArray User Guide provides detailed information for this step.

h5}}Step 3: Upload, validate, and import files into caArray.{{h5End
In this step, slightly different processes are used to load data into caArray for different array platforms.

• Step 3A: Import data under the MAGE-TAB format (Figure 4).
• Step 3B: Import experimental data using the Affymetrix platform (Figure 5).
• Step 3C: Import experimental data using the Illumina platform (Figure 6).
• Step 3D: Import experimental data using the Genepix platform (Figure 7).
• Step 3E: Import experimental data using the Agilent platform (Figure 8).
• Step 3F: Import experimental data using the ImaGene platform (Figure 9).
• Step 3G: Import experimental data using the Nimblegen platform (Figure 10).

h5}}Step 3A: Import data under the MAGE-TAB format (Figure 4){{h5End

Only file types listed in Figure 4 can be imported.
!Import-MAGE-data.JPG_!

h5}}Step 3B: Import experimental data using the Affymetrix platform (Figure 5){{h5End

Because of a known issue concerning importing Affymetrix DAT file, uploaded Affymetrix DAT files should be kept in the "Manage Data" tab under the "Data" tab for a selected experiment for caArray versions up to version 2.1.1. Once the issue is resolved, Affymetrix DAT files will be able to be imported the same way as EXP, RPT, and TXT files.
!Import-Affymetrix-data.jpg_!

h5}}Step 3C: Import experimental data using the Illumina platform (Figure 6){{h5End
!Import-Illumina-data.JPG_!

h5}}Step 3D: Import experimental data using the Genepix platform (Figure 7){{h5End
!Import-Genepix-data.jpg_!

h5}}Step 3E: Import experimental data using the Agilent platform (Figure 8){{h5End

Because of a known issue concerning importing Agilent TSV file, uploaded Agilent TSV files should remain in the "Manage Data" tab under the "Data" tab for a selected experiment for caArray versions up to version 2.1.1. Once the issue is resolved, Agilent TSV files will be able to be imported the same way as TXT files.
!Import-Agilent-data.jpg_!

h5}}Step 3F: Import experimental data using the ImaGene platform (Figure 9){{h5End

Because of a known issue concerning importing ImaGene TIF file, uploaded ImaGene TIF files should remain in the "Manage Data" tab under the "Data" tab for a selected experiment for caArray versions up to version 2.1.1. Once the issue is resolved, ImaGene TIF files will be able to be imported the same way as TXT files.
!Import-ImaGene-data.jpg_!

h5}}Step 3G: Import experimental data using the Nimblegen platform (Figure 10){{h5End
!Import-Nimblegen-data.jpg_! |</noinclude>

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