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Analysis of Microarray Data

e of ribosomal RNA could have cumulatively skewed the detection and quantification of genes that were expressed in very low amounts when mRNA or total RNA was used.

Figure 7. Scatter Plot Analysis of all Array Elements. A scatter plot of the Cy5 vs. Cy3 values obtained for an aRNA and a mRNA array is shown. The top two panels depict the 6 clusters (obtained after K-Mean Clustering Analysis) containing all 6912 elements. A subset of elements that are distinct between the two arrays and which deviate the most in signal intensity are depicted in the lower panels.


Amplification of RNA thus provides a means of measuring expression from genes transcribed at very low levels. In many cases the RNA concentration of an experimental sample is under the optimal required amount for synthesizing labeled cDNA for microarray analysis. MessageAmp is a viable technology for increasing the yield of useful probe and can greatly lower the starting amount of RNA required to produce biologically relevant signals.


More on Microarray Analysis
In future columns we will continue to report results from MessageAmp microarray studies from Ambion researchers, our collaborators, and our customers. If you have results you would like to share, please contact Lakshmi Madabusi at lmadabusi@ambion.com or call 1-800-888-8804 x6308.


REFERENCES

1. Quakenbush J (2001). Computational analysis of microarray data. Nature Reviews Genetics. 2(6): 418427.

2. Tavazoie S, Hughes JD, Campbell MJ, Chos RJ and Church GM (1999). Systemat
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