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Affy Regional Bias Quality Control

Usage: Please upload one zip file of less than 44MB size, containing between 5 and 15 CEL files. At the moment not all chip sizes are supported. If you get a message that your chip size is not recognized, please send e-mail to

Interpretation:The programs give three types of QC information. All programs are written in R, and are built on the affy package of Bioconductor.

The first program produces images that show regional biases on each Affymetrix chip. The upper left square of each image shows the raw intensities of probes on a log scale. The upper right square shows the intensities of probes relative to the average of all chips in the series. Regional biases show up as red (high) or yellow (low) regions. The lower left image shows changes in local background relative to the average, and the lower right image shows changes in local scale factor - how much signal per amount of RNA. For more details click here.

The second program produces a plot of the distribution of ratios to standard for each chip in a different color. This shows changes in dynamic range of the chips, usually an artifact. Quantile normalization can compensate such artifacts somewhat, but not fully.

The third program is a nicer visualization built around the AffyRNAdeg program written by Rafael Irizarry, and available through the affy package.

Download: To download the code, click here.

You will receive an email message with instructions on how to download your results once they are complete.

Your E-mail Address:
Your cel File:
Select your images
bias images
ratio images
RNA degradation profiles

SmudgeMiner is a development of the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR) National Cancer Institute (NCI). If you have any problems, questions or feedback on the tool, please email us.