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Figure 3 | BMC Neuroscience

Figure 3

From: Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method

Figure 3

Graphs displaying the variability of the data at different levels of replication; In all graphs one dot represents one gene. Panel A) shows MA-plots for each comparison. The x-axis represents the intensity of the feature (A = 1/2log2(Cy5*Cy3)). The y-axis represents the magnitude of differential expression of the gene (M = log2(Cy5/Cy3)), calculated after filtration and normalisation of the data. Dotted lines are drawn at M-values 1 and -1, i.e. at a 2-fold difference in signal intensity between the compared samples. Panel B) shows volcano plots for each sample. The x-axis shows the M-value for each gene and the y-axis the corresponding B-value (calculated by empirical Bayes moderated t-test) for that gene. Panel C) shows scatter plots for each comparison. The x-axis displays the average signal intensity for one sample and the y-axis the average signal intensity for the other sample. Also shown are the values of the Pearson correlation coefficient (r) and the coefficient of determination (R2).

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