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Our study has been constrained by the availability of transcriptional data sets publically available on a coherent microarray platform (the integration of data sets deriving from different technologies would have introduced too much noise in the meta-analysis).
As microarray platform, the 4 × 44 k design from Agilent (CA, Santa Clara, USA) was chosen.
The microarray platform the sample data comes from is the AffymetrixGeneChip Arabidopsis ATH1 Genome array.
In this microarray platform, the sample miRNA was labelled with Cy5, while spike in oligos were labelled with Cy3 for data normalization.
To calculate the resolution of a microarray platform, the outcome of the power analysis is used in conjunction with the genomic coverage of the platform.
Although these kinds of international trials can lead to the use of a standard microarray platform, the introduction of the technology in routine clinical application is still debated.
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Gene expression analyses were performed using two different microarray platforms: the in-house manufactured 29K oligonucleotide microarray platform and Agilent SurePrint G3 platform.
Information about these datasets, such as microarray platforms, the number of samples available, etc, is listed in Table 2.
Here we present results from investigation of two commercial microarray platforms, the Affymetrix system and the Incyte Genomics system.
For different microarray platforms the spotted probes are synthetic oligonucleotides ranging from 25 to 80 nucleotides or long cDNA transcripts.
However, by increasing the training compendia to a large number of samples with multiple microarray platforms, the algorithm's dependency on the datasets or microarray platforms can be greatly reduced.
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