Affymetrix Users - Data Retrieval

You will soon receive a CD containing data from your Affymetrix transcript profiling experiment. Microarray Suite v 5.0 users can copy the .dat and .exp files into the Testdata folder in your GeneChip directory. After copying, select all the transferred files and right click to open the Properties window. Uncheck "read-only," then Apply. The CD also contains text files of results for all genes, quality control measurements, and pairwise comparison results if applicable.

The QC worksheets (Excel file) report quality control results for each chip; we pay most attention to:

Scale factor - an outlier would indicate a chip with much higher or lower overall signal compared to other samples. Scaling factors are usually less than 4. Percent genes called present - should be greater than around 35%. 3'/5' for GAPDH - in human samples, the GAPDH housekeeping gene seems to be the best indicator for full length cDNA production. GAPDH and beta-actin are appropriate indicators for mouse samples. Ratios are usually less than 3.

The tab-delimited text files contain all the metrics window outputs after GeneChip quantitation in MAS 5.0. See Single Array Analysis at Affymetrix Statistical Algorithms Reference Guide. These files are suitable for importing into Excel, GeneSpring, GenoMax and other transcript profiling analysis packages. Global scaling (target = 150) has been applied to allow direct signal comparisons between samples.

If a pairwise comparison was appropriate for your experiment, these results are in an Excel file. See the Comparison Analysis section at the above link. A common way to organize such results is to filter out genes called No Change (NC), filter out those called Absent (A) on both GeneChips, and then sort by the Change P-Value and/or Signal Log Ratio.

Netaffx Analysis Center provides a database of probe information and annotations.

Last Updated on 9/3/03