PLM Image Gallery

A Rogues Gallery
Maintained by Ben Bolstad
The goal of this website is to show some of the interesting artifacts observed in the chip pseudo-images produced by the PLM procedures in the BioConductor affyPLM package or via RMAExpress. The hope is that an explanation can be given for each artifact. The goal is to increase user understanding of, and ability to detect, potential quality issues with their data. Contributions are most welcome (anonymity will be preserved). One way to create the necessary output using affyPLM is the PLMImageGalleryScript.R script. Please email me for more details on what you should submit bmb@bmbolstad.com
You can read more about how to use affyPLM from BioConductor to produce similar images in:
Bolstad BM, Collin F, Brettschneider J, Simpson K, Cope L, Irizarry RA, and Speed TP. (2005) Quality Assessment of Affymetrix GeneChip Data in Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S. (Eds.), Springer, 2005. Publisher Website
Or the software documentation: affyPLM: Model Based QC Assessment of Affymetrix GeneChips
Interesting Images
NameSample Image
Crop Circles
Affy U95A Spikein
Ring of Fire
Tricolor
Moon shape
Arcs
Assessment of Complete Datasets
NameImages
Affymetrix U95A Spike-in Dataset Image GalleryAssessment Plots
E2A-PBX1 Image GalleryAssessment Plots
Rat Dataset Image GalleryAssessment Plots
Different Sites Image GalleryAssessment Plots
Test Chips Image GalleryAssessment Plots
Spastic Mouse PEPR dataset Image Gallery
St Jude ALL Dataset 1 Chips Image Gallery
St Jude ALL Dataset 2 Chips Image GalleryAssessment Plots
St Jude ALL Dataset 3 U133A Chips Image GalleryAssessment Plots
St Jude ALL Dataset 3 U133B Chips Image GalleryAssessment Plots
St Jude ALL Dataset 4 Chips Image Gallery
St Jude AML Dataset 1 Chips Image Gallery
GSE1588 Time Series Data Image GalleryAssessment Plots
Estrogen Dataset from BioConductor Image GalleryAssessment Plots
Drosophila Embrogensis Time Course Image GalleryAssessment Plots
Systematic Scratch Image GalleryAssessment Plots
Arcs Image GalleryAssessment Plots