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Analysis of Microarray Data

total score was calculated to be 1.082e+004. The most closely clustering genes had a similarity value of 0 and the least similar gene had a similarity value of 1.798e+308.

Figure 6. An analysis of variance calculation of K-mean clusters 5 and 6. This plot indicates the confidence limit of the data. A p-value, of less than 0.0001 was used, indicating that the genes represented in this plot are unique at the 99.9999% cut-off value.


Analysis of variance (ANOVA) of genes in clusters 5 and 6 indicated that the clusters contained genes that behave distinctly between the mRNA and aRNA samples at a confidence limit of 99.99999% (p<0.00001). ANOVA measurements processed the gene-by-gene fluctuations from the mean value and accounted for variance across samples.

A scatter plot analysis of the raw Cy3 and Cy5 values of all the 6912 elements within the 5 gene clusters is shown in Figure 7 (4 plots). The top two plots represent all the elements and the bottom two depict the genes that show the largest differences in signal. Most of the genes that are distinct between the samples are expressed at lower levels (low fluorescent signal). These differences were more exaggerated in the aRNA than the mRNA sample because the signal-to-noise ratio was typically much greater in the aRNA sample. The distinct genes in the aRNA panel might be elements that were not clearly discernible in the mRNA sample due to ribosomal contamination (27% in the mRNA used for this analysis). The presence of ribosomal RNA can increase background in mRNA samples, resulting in variations in mRNA concentration between samples and decreasing the efficiency of cDNA probe synthesis. Thus the presenc
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