Upload probe files to eArray

One way to introduce new microarray probes into eArray is to upload a file of probes. You can upload probe sequence and annotation data to eArray, and use the uploaded probes to create a new probe group, or add the uploaded probes to an existing probe group. Later, you can use the probes to create a microarray design.

When you upload probes to eArray, you submit data to a database. The purpose of a database is to store, and to let you search, unique records. If your uploaded file contains duplicate probes, you can mark the Remove replicate probes from upload option, and eArray removes the duplicates.

eArray can guide you through the process of creating a microarray with uploaded probes. See Create a microarray design by uploading probes (Wizard). In addition, you can use the Express Array feature in eArray to upload a file of probes directly to Agilent Manufacturing.

Note:
• Probe upload is not available for microRNA probes.

• You cannot upload probes as certain specialized probe types, such as SNP, Exon, or lincRNA probes.

Before you upload

You must be a registered user in eArray.
Your probe file must satisfy certain requirements. See Probe file formats and requirements for uploading.

Note: Upload no more than 200,000 probes at a time to eArray. Probes from very large uploaded files may not appear in your account for an extended period of time.

To upload probe files

Click the Workspace tab, or enter a collaboration.
Set the application type, if needed.
Click Probe > Upload.

The Probe Upload page appears.
Specify the following parameters. All are required.

Parameter	Instructions/Details
Probe Parameter Details
Species	Select the desired species from the list. If you do not want to select a species, or if the desired species does not appear in the list, select Na.
Remove replicate probes from upload	A replicate probe has the same Probe ID as another probe in the file. If you mark this check box, eArray uploads the first probe in each set of replicate probes in your file, and ignores the others. Note: If your probe file contains replicate probes, and you do not mark Remove replicate probes from upload, eArray displays an error message after you begin the upload, and does not upload your file.
Probe Precedence	These options specify what eArray does if it finds probes in your uploaded file that match (have the same Probe ID and sequence as) probes that already exist in the system. Select one of these options: Overwrite matching probes – The annotation of the matching uploaded probe replaces the annotation of the existing probe. You can use this option to re-annotate existing probes. Skip matching probes – eArray ignores the matching uploaded probe. Cancel upload if any probes already exist — eArray cancels the entire upload process if it finds a matching uploaded probe.
Upload Probe File Details
Upload Type	Select one of these options: Upload Probes Only – Creates probes from the data in the uploaded file, and makes them available to you in eArray as individual probes. Create New Probe Group – Creates probes from the data in the uploaded file, and puts all of the probes into a probe group. Type a name for the probe group.
Upload File	Click Browse. A dialog box appears. Select the desired file for upload, then click Open. The name of the file appears in Upload File.
File Format	Select MINIMAL or COMPLETE. The file format defines the specific types of data available in the uploaded file. See Probe file formats and requirements for uploading.
File Type	Select the appropriate file type from the list. The file type defines how the data items in the file are specified and separated. eArray accepts tab-delimited text (.tdt and .txt) and MS-Excel (.xls) files. Note:* If you use Microsoft Excel 2007 to create the file, save the file as an Excel 97-2003 workbook. This saves the file in the required *.xls format.

Click Next.

The Define Upload File Columns pane appears at the bottom of the page, with a preview of the first few lines of data in your file.
eArray does not interpret any existing column heading data in a probe file. If the first row of your probe file is actually a row of column headings, mark My uploaded file contains column headings, so eArray does not interpret the column headings in the file as a set of probe data.
In the Define Upload File pane, from the list below each column, select the label that best matches the data in the specific column above it.

If you want the upload process to ignore a specific column, select Ignore. Use each label exactly once, except Ignore, which you can use any number of times.
Click Upload.

eArray processes the uploaded file, and creates the probes. If you selected Create New Probe Group, it also creates a probe group. Be sure to read the introduction to this topic for information about probe groups and duplicate probes.

A message informs you that your file was successfully submitted to the upload queue, and that eArray will send you an e-mail when the upload process is finished.
Click Close.

You can monitor the progress of the upload in the Pending Jobs pane on the workspace home page. After eArray finishes your upload, you can search for your new probes and probe group, and use them in microarray designs.

The Probe Upload page appears, and you can set up another probe file upload.