Skip to main content
Figure 6 | BMC Ophthalmology

Figure 6

From: Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies

Figure 6

Composite image of Quality Control metrics applied in Gene 1.0 ST array. Image A is of an Agilent assay of a RNA sample showing two peaks 18S and 28S of ribosomal RNA. Image B is of the nanodrop spectrophotometer, the plot shows a good curve with 260/280 optical density ratio in the range of 1.8 to 2.2. Image C is of a nanodrop spectrophotometer plot of fragmented cDNA. The fragmentation efficiency of the fragmented sense strand cDNA was assessed with nanodrop. The fragmented cDNA peaks for the samples checked on Agilent Assay ranged between 40–70 NT (nucleotides); indicating efficient fragmentation of the samples. Image D is a box plot of probe cell intensities generated from the CEL file probe intensity values of all the 12 arrays before normalisation of the data. The expression intensity values are distributed around the median intensity values of the entire samples box plot. Image E is of a scatter graph plot of Pos_vs_neg_auc values across the samples. As seen in the figure all the samples were above the minimum criteria of 0.8. Image F shows MvA plot comparing two arrays 898(2) limbus and 798(1) cornea. The arrays show a good correlation of the expressed genes. The colour coding of the plot denotes the density of the signal probes represented by that data point. Y-axis represents the M values that display the differences in the log signals of the arrays and X-axis represents A values which is the average log signal. The green lines are the threshold lines for +/− two fold changes. The genes expressed around the baseline 0.00 are unchanged genes between the two arrays.

Back to article page