spotSegTest: Spot Segmentation Test Data

In spotSegmentation: Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots

Description

The two columns of this data set represent the Cy3 (green) absorption intensities for channel 1, and the Cy5 (red) absorption intensities for channel 2 for part of a dye-swap experiment with replicates. They measure expression levels of cellular RNA transcripts assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays.

Usage

data(spotSegTest)

Format

Each column is a vector of intensities of 24 spots arranged in 4 rows and 6 columns, encoded for compact (16-bit TIFF) storage. For processing each column of spotSegTest should first be converted to a 144x199 matrix, then applying the transformation described below.

Details

The intensities can be obtained from this data by first subtracting them from 65535 (256*256-1), then squaring, then multiplying by a scale factor 4.71542407E-05. In other words, a number x in the spotSegTest data set corresponds to intensity

(256*256 - 1 - x)^2*.0000471542407

. \

Source

Dr. Angelique van't Wout, Department of Microbiology, University of Washington\ The data is a subset the first block of a 12 block array image (001030\_08\_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr) of the following data archive:\ http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html

References

van't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI\ Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines.\ J Virol. 2003 Jan;77(2):1392-402.

spotSegmentation documentation built on April 28, 2020, 9:18 p.m.