2.2. FlexmiR MicroRNA Human Panel
A total of 319 human miRNAs are profiled using the bead-based Luminex FlexmiR MicroRNA Human Panel (Luminex, Corp., Austin, TX, USA) for 40 treated and untreated osterosarcoma xenograft specimens. Due to the capacity of the pool, all miRNAs are divided into five groups and are tested using five different human pools separately. The intensities are captured with a Luminex-200 instrument. In addition, for each microsphere type being tested, a background control (water treated in the same manner as an RNA sample) is used to measure the background signal (median fluorescence intensity, MFI). The system does not flag results based on the signal quality. For the 40 profiles based on the treated and untreated samples, we manually flag the signals of different miRNAs as follows: we compute the standard deviation, s, of the background signals for each pool. If the signal of an miRNA after background subtraction is smaller than 2s. but not smaller than s, we flag the miRNA as weakly expressed; if the signal of an miRNA after background subtraction is smaller than s, we flag it as empty; otherwise, an miRNA is not flagged. Table 3 shows the percentages of miRNAs based on all 40 profiles. From Table 3, we find that about ∼60% or more miRNAs have reasonably strong intensity measures across all 40 arrays. In the worst case, the total percentage of weakly or not expressed miRNAs is about 40%. In summary, compared with the LNAv7 and LNAv9 arrays, the signal quality of the bead arrays is much improved, as expected. But on the other hand, we see that the percentage of weakly or not expressed miRNAs is high in arrays from all three platforms.
microarrays-02-00034-t003_Table 3 Table 3  Quality flags with FlexmiR bead arrays.

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