Wednesday, January 13, 2010

RLE AND NUSE plots

Affy QC plots for exon arrays ...

One method of deciding whether or not an array is problematics from a quality standpoint is NUSE. The goal of NUSE is to identify any arrays which have elevated standard errors relative to other arrays in the dataset. This is done by standardizing the SE across arrays to have median 1 for each probeset. Our graphical tool consists of boxplots of these quantities for each array. A discordant boxplot indicates it is of poorer quality relative to the rest of the dataset. Instead of visually examining these quantities suitable numerical summaries such as the median and IQR NUSE could be used.

Another tool for making a decision about whether an array should be removed from subsequent analysis because of poor quality is RLE. These are the log-scale expression values relative to the median expression value computed on a probeset by probeset basis. a significantly different boxplot indicates problem.

aroma.affymetrix and other lots of packages allows to plot RLE and NUSE.

The NUSE is generally considered more sensitive than the RLE.

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