Detecting Spatial Patterns in Biological Array ExperimentsOverview
Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here we apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random background. We demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microtiter plate assay data. In addition, we employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided.
All of this information is associated with the paper "Detecting Spatial Patterns in Biological Array Experiments".(pdf)Downloads
"VisTa" Spatial Pattern Analysis Software:
(principal developer/ contact person Brian Kelley)
Our software (VisTa) incorporates one of the many freely available software packages for computing the DFT. VisTa reads many standard plate reader files and all files in comma seperated values (.csv) format. Plate can be of any size. This is a windows download. You will need to uncompress the installer file before installing VisTa. (VistaInstaller)
"SLIMS" Small Laboratory Information Management System:
(principal developer/ contact person Brian Kelley)
A complete information managament system containing all the functionalities of Vista as well as numerous other features. (SLIMS)
