The Affymetrix GeneChip® Laboratory is a Purdue Cancer Center Shared Resource.
How to contact us:
Array Coordinator: Ann Feil.
Ann's email: afeil@purdue.edu
phone: 67368 (Affy Facility) or 66329 (High Throughput Laboratory)
Genomics Core Director: Phillip SanMiguel
phone: 66328
Phillip's email: pmiguel@purdue.edu
Please contact Ann Feil prior to bringing RNA samples for GeneChip® Analysis.
As of January, 2008 we are using new Enzo kits for cDNA/cRNA synthesis. These Enzo kits are incompatible with certain Qiagen kits that you may be using for sample prep. So if you are thinking about using Qiagen kits then please consult with us. To be more precise, it is the 'polyA RNA carrier' that is used in extracting total RNA from small samples (such as in the Qiagen RNeasy Micro Kit) that is incompatiable with the VanGelder/Eberwine methods such as we use from Affymetrix and Enzo.
Results
Access to the results below will require your LTL (low throughput) password. These results are just the raw data files. You will need to do the analysis via the methods outlined below. As of Apr-2005 all files are being bundled together into the CAB format that is used by the Affy GCOS software. This format can be read by GCOS, WindowsXP and many un-zip programs. As of Aug-2005 a tab-delimited text file is also generated. You can use this file in a spreadsheet program.
Click on your last name in order to retrieve your results
| Customers | LTL | FL | Genotyping | Affy | All services |
|---|---|---|---|---|---|
| Genomics personnel only | LTL | FL | Genotyping | Affy | All services |
| Chapple, Clinton C. | |
| Gelvin, Stanton B. | |
| Hasegawa, Paul | |
| Kaczorowski, Karen | |
| Muir, Bill | |
| Newcomer, Sean | |
| Pittendrigh, Barry R. | |
| Salt, David E. | |
| Szymanski, Daniel B. | |
| Woloshuk, Charles P. | |
| Xu, Jin-Rong |
Analysis
The first step -- which is image analysis in order to get the results from the raw image data into a spreadsheet compatible format -- should be done via Affymetrix's GCOS software or via 'Bioconductor/R'.
The important statistical steps can be done via 'Bioconductor/R' or 'SAS microarray solutions.' This software is available at the Genomics facilty. Get hold of our system administrator Doug Yatcilla if you need an account on our computers.
Another option is to use the Purdue Statistical Consulting Service (SCS) which can provide personalized help in your analysis. Bruce Craig is one person at the SCS who knows a lot about microarrays. Please note that we do not automatically forward your samples and CAB files to the SCS. You are responsible for doing so.
Yet another option is for your lab to do the statistical analysis via the Affymetrix GCOS software yourself. Here are some instructions on how to install the software on your own PC. You will need to install your genome library which involves yet another step.
No matter which of the statistical methods above that you use make sure that your data is all scaled and normalized using the same parameters. It is probably obvious that this should be done. However we have seen erroneous results because of failure to do the same scaling & normalization either in the conversion of the image to spreadsheet compatible data (via GCOS) and/or in the statistical analysis stage.
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| Affymetrix microarray home | ||||
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