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To avoid complications from the comparison between different platforms, we only used measurements from the Affymetrix ATH1 GeneChip platform.
Since expression measures are not directly comparable between different platforms we used the Rankprod approach [ 25] that is based on log2ratio ranks.
Since expression measures are not directly comparable between different platforms we used the RankProd approach [ 39] that is based on differential gene expression ranks.
To assess the correlation between different platforms, we first set cutoffs to select subsets of genes with discernible expression signals for each platform.
To enrich the CNV calling and compare the detection performance between different platforms, we performed an alternative aCGH-based CNV identification by a custom-designed 1M aCGH produced by Agilent Technologies.
In order to avoid the problems caused by bias between different platforms, we only used the intersection of the results from these five expression datasets, which cause that 233 up-regulated genes and 286 down-regulated genes left (see Figure 1).
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To assess the degree of similarity between the aberration patterns found with different platforms, we consider the ability of each platform to mimic the other two platforms' classification of genomic loci.
As different microarray platforms have different approaches on how to sample the transcriptome, and about how to represent the concept of 'genes', the details may differ between different platforms.
We assert that differences in platform sensitivity, reproducibility and annotation cross-referencing accuracy account for a majority of the irreconcilable differences previously reported between different platforms [ 4- 7].
"It's similar to Kickstarter, where people are trying to crowd fund the development of the network, but the difference here is that … there's a significantly different risk between different platforms in crypto vs. a product that just needs manufacturing," he says.
This event also led to more integration between different platforms as well.
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