Moreover, we believe this should not be done, as effects of technical differences between the platforms would then have been ignored, which is undesirable.
Appreciation of the basic differences between the platforms is crucial for understanding the differences in performance.
The differences between the platforms are stark.
The mean difference between the platforms is low (of the order of 1 dB), with standard deviation of differences between 7.1 dB (VG-MAN) and 5.6 (MAN-HFA).
Array-based genomic comparisons can also identify orthologs with high sequence divergence because an increased number of basepair differences between the platform species and the heterologous species will cause a detectable reduction in hybridization strength for the heterologous species [ 40, 41].
** The number of differential genes obtained comes from the integrated analysis of data from all platforms within one statistical model which takes the platform into account (cf. Discussion section) There was a large difference between the platforms in the number of probes which generated a signal above background.
As expected, and in agreement with the correlation analysis, the difference between the platforms was responsible for the majority of the overall variance in raw (58%), quantile-normalised (47%), and mean-centered (44%) expression data.
The reason for the app differences between the two platforms remains a hot topic of debate.
It is also important to note that because of differences between the two platforms [e.g., non-overlapping nucleotide sequences for the same transcript targets as well as different hybridization conditions for the 1.5K and 24K assays (as described above)], direct comparisons of the raw intensities will yield seemingly poor cross-platform correlations.
In our study we included results from both Illumina RNA-seq and SOLiD RNA-seq, revealing differences between the two platforms largely due to the method of rRNA exclusion in library construction.
