Re-annotate probes

Over time, probe annotations can change, and Agilent updates catalog probe annotation automatically on a regular basis. You can use the Re-annotate tool in eArray to obtain updated annotations for your own probes at any time. eArray aligns the sequences of your probes to the applicable genome, and then associates the most recent annotation available from public databases. To specify the probes to be re-annotated, you either upload a file of probes, or select one or more probe groups. eArray produces a TDT file that you can download that contains your re-annotated probes. Currently, eArray supports re-annotation of probes for H. sapiens, M. musculus, and R. norvegicus targets.

Note:
• The Re-annotate function produces a TDT file of re-annotated probes, but it does not update any of your probes in the eArray system. To update your probes in the system, you must upload the re-annotated probes. Be sure to select the Overwrite matching probes option. See Upload probe files to eArray.

• Probe re-annotation is available only for the Expression and CGH application types.

• You cannot re-annotate Agilent Catalog probes, or probe groups that contain Agilent Catalog probes.

Before you re-annotate probes

You must be an eArray registered user.
The probes to be re-annotated must be CGH or Expression type probes.
You must either have a probe group in eArray, or a TDT (*.tdt or *.txt) or Microsoft Excel (*.xls) file of probes in MINIMAL format. See Probe file formats and requirements for uploading. The Re-annotate tool uploads your probe file without the opportunity for you to label columns. Therefore, the first column must contain probe IDs, and the second column must contain probe sequences. Also, do not include extra columns, or a row of column headings in your file. 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.

To re-annotate probes

Click the Workspace tab, or enter a collaboration.
Set the application type to Expression or CGH.
Click Probe > Re-annotate.

The probe re-annotation page appears.
Set the following under Job Details:

Parameter	Instructions/Details
Re-annotation Job Name	Type a name for the re-annotation job. eArray uses this name to reference the job in search results, lists, and the like.
Probe Type	(Read-only) eArray defines the probe type based on the application type you set earlier.
Species	Select the species that is associated with your probes.

Select one of the following options:

Option

Instructions/Details

Upload Probe File

Obtains annotation for probes contained in a TDT (*.tdt or *.txt) or MS-Excel (*.xls) file.

Click Browse.
A dialog box appears.
Select the desired probe file, then click Open.
The location of the file appears in Upload Probe File.
In File Type, select the option that matches the format of your file.

Probe Group

Obtains annotation for probes contained in a probe group in eArray.

To select a probe group for re-annotation:

Click Select and Add.
A probe group selection page appears.
Select one or more probe groups. For instructions on how to use this page, see Select probe groups for probe searches.

Click Re-annotate.

A message informs you that your re-annotation request has been submitted, and that you will receive an e-mail when the process is finished.
Click Close.

eArray processes your request and reannotates your probes.

You can monitor the status of your re-annotation job in the Search Results pane. In the Status column, several designations can appear:
- Pending – Your job has been submitted, but re-annotation has not begun.
- Processing – eArray is reannotating your probes.
- Complete – eArray has finished the job, and the results are available for your use.

When your job is finished, you receive an e-mail. On the Re-annotation page, in the Search Results pane, your probe re-annotation job has a status of Complete, and several links appear in the Actions column.

You can take several actions on the results of your completed probe re-annotation job.

Task	Instructions/Details
View probe reannotaion report	You can view a summary and details of the probe reannotaion job. In the Actions column of the search results, next to the desired re-annotation job, click View. The probe annotation report appears. Click any of these tabs to see the different parts of the report: Annotation Summary – General information about the job, including statistics on the number of probes submitted, and the number of probes that were removed. Annotation Details – A list of the first 100 probes with their updated annotation. To see more than 100 probes, you must download the results (see below). Annotation Fate – A list of the first 100 probes, with information about which probes were re-annotated and which were not. To see more than 100 probes, you must download the results (see below).
Download re-annotation results	You can download the results of the probe re-annotation job. In the Actions column, next to the desired job, click Download. A dialog box appears. Click Save. A Save As dialog box appears. Select a location for the file, then click Save. eArray downloads a ZIP archive that contains these files: eArrayCustomAnnotationData.tdt – a TDT file of re-annotated probes. The file is in COMPLETE format. For details on this format, see TDT format files. ProbeCuration_fate – Tab-delimited text file that contains a list of the probes, with information about which probes were re-annotated, and which were not. ProbeCuration_sum – Tab-delimited text file that contains general information about the job, including statistics on the number of probes submitted, and the number of probes that were removed.
Delete probe re-annotation job	You can delete the probe re-annotation job from eArray. When you delete the job, you can no longer view the results, and the results file is no longer available for download. In the Actions column, next to the desired job, click Delete. A dialog box appears. Click OK. A message informs you that your job has been successfully deleted. Click Close.