Integration and standardization difficulties are compounded as basic information such as SNP IDs (e.g. names) are not consistent across array suppliers, and in some cases, not even between array releases from the same supplier.
In Figure 3 and in the bottom two subpanels of Figure 4, each data point is labeled with the (abbreviated) sample number as in Tables 1 and 2, indicating a consistent sample array from AW-2, which is closer to or almost on the meteoric water line, to AW-11, which is closer to magmatic water.
Expression ratios by qRT-PCR were highly consistent with array values and overall somewhat higher by qRT-PCR as expected.
The validation data were consistent with array results, indicating the up-regulation of five miRNAs and down-regulation of four miRNAs.
Overall, the expression patterns of the NBS-LRR-encoding and related genes detected in the above microarray experiments were generally consistent among array experiments.
Also, since parameters are consistent between arrays, there is no need to reprocess the early data when new samples are hybridized.
This artificially-created dataset contained only transcripts that were added in known concentrations, therefore the expression signals are likely to be much more consistent across arrays than signals from different individuals.
Therefore, the RT-PCR analyses on these seven published events were consistent with array-derived results except for exon 23A of NF1, which was not represented by an established RefSeq.
In all six cases, the bisulphite sequencing results were consistent with the array data, indicating that that the array is suitable for the identification of tDMRs.
A visual inspection of the distributions of raw perfect match (PM) probe-level intensities for all 18 arrays showed that pre-processed and normalized PM intensities using Robust Multi-Array Average (RMA) [ 30] were consistent across all arrays with no apparent outlying arrays.
