Test Chips Assessments Plots

Date: October 5, 2004
Submitter: MA Hannah, AG Heyer, DK Hincha. Max-Planck Institute of Molecular Plant Physiology, Golm, Germany.
Chip Type: ATH1 and Test chips
Fitting Function: fitPLM with default background and normalization
Comments From the Submitter: We had a chip that was an outlier in comparison to the rest of our dataset (hist(affybatch), RNAdeg, AffyPLM). All our samples are hybridised to test chips before hybridisation to ATH1 arrays. This sample passed the Affymetrix QC based on the test chip 3:5 ratios and scaling factor (although this was slightly higher than normal).

In the post-mortem I decided to fit a PLM model to the test chips and the same sample was also an outlier (very green in the image plots). This is despite the fact that only a small proportion of the test chip probesets are against arabidopsis (clearly the NS binding was sufficient). This helped to clearly identify that the labelling had failed, rather than it was just a bad ATH1 chip.
Comments From the Maintainer: The first NUSE plot is for the ATH1 chips and the second for the Test chips. The first RLE plot is for the ATH1 chips and the second for the Test chips.
Other plots : Weights and Residuals pseudo-chip images
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