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Figure 7 | BMC Bioinformatics

Figure 7

From: Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data

Figure 7

Pixels of unusually low intensity and their influence. (A) Illustrating the occurrence of an unusually low intensity pixel. A region, centred on pixel (964, 6081), from image 4343238066_A_2_Grn.tif, is illustrated. Whilst the majority of the image shows the typical background log-intensity, a single pixel with an incredibly low value is observed. Note that this occurs in the vicinity of an almost-saturated high-intensity bead. Seven beads which include this pixel in their background region have been successfully decoded, and their bead-centres are indicated. (B) Illustrating how the intensities of the affected beads show a large deviation from the summarized value for their respective bead-types. If the median of the five lowest pixels is used instead of the mean during the background calculation, the impact of the low intensity pixel is reduced in most cases.

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