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What are scatter plots?

April 26, 2017plots scatter

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What are scatter plots?

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The scatter plot is one of the simplest methods used to visualize overall mRNA expression levels within a single hybridization. The M-A scatter plot is a convenient to observe the distribution of intensity values and log ratios. M-A scatter plots are provided for each array and for separate blocks of each array. The colored lines appearing within the scatter plot represent the average for each print-tip-group and are drawn for the raw data and the processed (filtered and normalized) data. The M-A scatter plot is a Log2ratio (log2(cy5/cy3) ) vs. log2 intensity (1/2(log2(cy5*cy3))) plot. Therefore, if a gene has equal expression values in both the control and experiment, the expression ratio ( log2 ratio) will be zero. For a typical hybridization experiment, most genes will have equal expression values in both control and experiment and we expect the majority of points to be grouped around the horizontal line Y=0. Without normalization, the majority of points may be clustered around a ho