MA3 Manual

From CLAB

MicroArray Data Analysis Manual (Full Version)

[edit] MicroArray Data Analysis Manual (text version)

Quering the database:

Initial Screen (Query Database screen):

Select the organism from the dropdown list and click on select.

Select one control experiment from the left box. This automatically removes this experiment from the right box.

Then, you can select any number of experiments from the right box. You can click on the “check to select all experiments” to select all the experiments in the right box.

You can edit the fold value (which is by default ‘2’) to identify the outliers.

Selecting probeset Names:

You can choose one or multiple probesets from the list or use a list of probeset names separated by commas and paste it into the text box provided.

Generating outlier report for all the probesets:

If you click on the “check to select all Probes” checkbox, this will select all the probesets. Hitting the search button will

Data Analysis Output page

Show Experiments : Display the experiments selected for the analysis.

If you are using Mozilla/Firefox click on ShowPorbeSets on Target to view the graphical representation of the Analysis.

FoldValue: Enter a different number and hit enter to view the analysis for a different fold value.

Select various probesets from the dropdownlist of click on ‘previous’ or ‘next’ to iterate through the selected probesets.

On the flash display of the analysis,

Move mouse over the probes (green boxes) to get more info on that probe. The red boxes at the bottom represent the outliers. The probe number box on the top right displays the probe order for the current probe.

The probes are ordered in ascending order of their start/begin value. This is the point in the target sequence whose length is proportional to the gray bars, where the particular probe sequence begins. The number on the top gray bars indicate the start which is always one and end of the target sequence of the particular probeset.

Adding new experiments/organisms:

Click on the Add Record button on the top.

Click on the browse button and find the Ver 4 experiment file with the “.cel” extension.

Once you have selected the file, click on upload once. Wait for the file to be uploaded which may take 2-5 minutes.

The page will automatically redirect you to the status page after the upload.

The experiment file you uploaded will be visible on the status page.

The status of the will be displayed in the status column. If the status is in red, it is being processed or something is wrong.

If the experiment file is not displayed on the status page, please try to upload the file again or contact the administrator.

Once the experiment file as been processed, the status should say “Populate data from experiment file complete.”

If the experiment is for a new organism, files associated with the organism have to be uploaded. Click on the upload organism info link to upload the new organism files.

Organism target seq file: This file is the target sequence file of the organism ProbeTable file: Probeinfo file: This is a .csv file

All the three files are required for the organism to be successfully added to database.

Please give it some time (depending on the upload speed of your connection) 2 to 10 minutes. It will redirect to the status page once the upload is complete.

If the status still shows that the organism files need to be uploaded, try again and if it still fails, contact administrator.

VIEW FILES:

This section displays the reports that were generated in the past. If a report is running currently, the buttons are disabled.

You can download the report by clicking on the xls button or the www button.

You can delete unnecessary reports by clicking on the delete button.