Cluster Prism®

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DraculaTM (Deterministic Resource for Analyzing Chips Using Linear Algebra)
Castle Dracula is an online program designed to analyze Affymetrix gene chips. It does the following.
  • Generates a model relating the responses of individual probes, on the model's chip type, to each gene/transcript queried by the chip type.
  • Uses the output model to estimate the expression levels of genes/transcripts in tissue solutions when applied to that chip type. Outputs the results to a tab-delimited ASCII file that can be easily loaded to a spreadsheet.
  • Maps the background response of each individual array, thus making it easy to identify artifacts on each individual array.

Example of Background Mapping Using DraculaTM More DraculaTM Info.
Background Background variation of a good quality Affymetrix human hg133 gene chip. The background variation is rather minimal but there are contiguous dark and light regions that would not be associated with the expression level of any given transcript since the probes, for each transcript, are scattered over the chip. Each of these regions represents several unrelated transcripts. Such background variation is subtracted from the measurements of the probes in the associated regions in order to improve the estimation of the gene expression. Such regions are easy to see in this image.

For this particular example, there is little background variation, so a linear scale has been used for the display. If there is considerable background variation then it is usually preferable to use a logarithmic scale so that subtle variation is not drowned out by large variations in other parts of the chip due to large and/or dense artifacts. If there is very little background variation, the exponential scale enhances what variation there is. The linear scale is ideal for relatively little to mderate variation. DraculaTM can display background images using linear, logarithmic increase, logarithmic decrease, exponential increase, and exponential decrease scales.

About Dracula

How Dracula Compares With Other Methods for Analyzing Affymetrix Gene Chips (Entry N=132)

Dracula How To Run Manual

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