|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: These images are based on material from 4 samples. For each sample the images are ordered such that the ATH1 arrays are in the first row followed by the Test arrays in the second row.|
|Other plots : NUSE and RLE|
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