News and FAQ

1. What is your turnaround time for my submitted samples?
2. What, if anything, needs to be done prior to submitting samples for microarray analysis?
3. What happens if any of my submitted samples fail to pass the initial quality assessment or the requested sample amount/concentration requirements?
4. What happens to any left over or excess materials following return of my resulting data?
5. What sort of files can I expect to find on my resulting data CD/DVD?
6. Can I purchase Affymetrix chips directly from the Core Facility?
7. If I end up with excess/leftover arrays, will the Core Facility purchase them from me?
8. What happens if I have a defective GeneChip array? How will I know if an array is defective?
9. I am considering partially processing my samples myself. Where can I get protocols or manuals?

1. What is your turnaround time for my submitted samples?

Our workload can vary and the “current level” at the time of your submission depends on sample submissions that have occurred just prior to your submitted sample set (generally First Come – First Served). That said, our typical turnaround time is from 6 – 11 working days, with the average being closer to 7 working days from receipt of samples before the resulting data CD/DVD is mailed back to the user.

2. What, if anything, needs to be done prior to submitting samples for microarray analysis?

If a new user, we strongly suggest you speak with the Facility Manager concerning your experimental design for microarray analysis prior to bringing/sending us your samples or purchasing arrays. Additionally, please be sure to read the Sample Submission page for particulars and required forms.

3. What happens if any of my submitted samples fail to pass the initial quality assessment or the requested sample amount/concentration requirements?

If submitted samples fail to meet established prerequisites for the initial quality control or sample concentration/amount levels, further processing will be halted and the user will be contacted to see if they wish for us to continue or await a replacement sample submission. NOTE – if the decision to proceed is made on a questionably flagged sample, we will not be held responsible for poor processing yields and any secondary processing steps performed in an attempt to bring the yield up to the required levels will incur additional charges.

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4. What happens to any left over or excess materials following return of my resulting data?

Any left over arrays may be held in the Facility at 4°C for future work. NOTE – While all effort will be made to properly store and protect your excess or stored arrays while in our possession, the Facility will NOT be held monetarily liable for loss or damage to any user arrays stored in the Facility refrigerator. Any excess sample material (total RNA or DNA) or processing products (cRNA, PCR or hybridization cocktails) will be properly stored in the Facility’s freezers for up to three (3) months following completion of the initial study. Samples and derived processing products still left in the Facility past this three (3) month storage period are subject to unannounced disposal as deemed necessary by the Facility staff. If you want or think you might have future need for any of these materials, please make prior arrangements for return or collect said items when picking up your data sample results.

5. What sort of files can I expect to find on my resulting data CD/DVD?

Your resulting expression data CD/DVD will have DTT files. Please see instructions located on the resulting data CD/DVD for downloading and installation of the GeneChip Operating Software (GCOS), associated library files and the Data Transfer Tool (DTT) from the Affymetrix. Please be aware that only the .TXT files on the CD/DVD can be opened outside of the GeneChip Operating Software (GCOS) (link to Affymetrix GCOS page). To view the other files you must download the previously mentioned applications to a local PC-Windows computer (again, please see instructions contained on resulting data CD/DVD). You will then be able to view the .DAT (a raw GeneChip image/scan file), .CEL (a processed image file with calculated signal intensities assigned to each oligonucleotide "cell" on the GeneChip), .CHP (a spreadsheet like, text-based file containing the relevant signal values, absolute calls and p-values assigned to each gene on the GeneChip), .TXT (data in text format, tab delimited [same as .CHP file] for easy transfer to third party software), .RPT (a text-based file containing the quality control numbers for the experiment including percent present, presence of spiked controls, background, noise, etc.), and .EXP (a text-based file containing general experiment information such as sample name, date, etc.). Please call the Facility at (949) 824-5327 for problems encountered in or other questions concerning accessing your returned data.

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6. Can I purchase Affymetrix chips directly from the Core Facility?

From time to time either the Core Facility or other users may have a limited number of excess/specific array types on hand (please see below). Occasionally, we may be able accommodate users by selling these extra GeneChip arrays to other users. Unless otherwise specified, the pricing for these offered arrays will be the same as the Academic Tier 4 discounted pricing that Affymetrix originally sells the arrays for to all UC System users (ourselves included) plus an additional 7.75% sales tax charge. To see the current Affymetrix Tier 4 discounted pricing (before tax) for these various arrays please look at either the Expression or SNP/Mapping array pages of this website. Please check for potential array availability at the Facility prior to ordering your needed arrays directly from Affymetrix.

7. If I end up with excess/leftover arrays, will the Core Facility purchase them from me?

Unfortunately, as much as we would like to assist you in recovering funds for excess materials, we can’t directly purchase your excess/unused arrays and directly give you the funds. We are willing to assist you by offering your arrays to other users (at your determined pricing). If they elect to purchase said arrays, we will bill them for the arrays used (at your determined price). You will then have an equivalent monetary credit with the Core Facility for any future work performed by us for you. Alternatively, you could look for potential purchasers yourself and/or workout direct exchanges or team up with another lab looking to run the same type of array to share expenses.

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8. What happens if I have a defective GeneChip array? How will I know if an array is defective?

Arrays determined to be defective are replaced by Affymetrix free of charge. Core Facility staff will inform you when a GeneChip array is suspected of being defective. We will submit the suspected array on your behalf to Affymetrix for their assessment/confirmation. Assuming they agree that the array was defective, a like replacement array will be returned to the Core Facility for your use (warning this process can sometimes take up to a month to transpire). You will be notified upon arrival of your replacement array. If, in the meantime, you do not have an additional array to re-run your defective array’s sample on, you will have to wait for the replacement array to arrive. Be aware that you will be charged by the Facility for re-hybridization of your previously run sample, either onto the replacement or secondary array. NOTE – Affymetrix will only replace an array with exactly the same array type that was found to be defective (you can’t trade one array type for another). For more information please contact one of the staff within the Facility.

9. I am considering partially processing my samples myself. Where can I get protocols or manuals?

You may request protocols directly from the Affymetrix website. You probably will be asked to register an e-mail address and password before you can download their protocols or manuals, but it is free. While we don’t offer users direct training or classes on these protocols, we do try to assist independent users by offering timely responses to specific protocol questions (“timeliness,” of course, dependent on possible workload constraints of the Facility staff at the moment).