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(C) Normalizing the data using a Robust Multiarray Average (RMA) method to remove systematic bias such as platform-specific variations or the influence of non-biological factors.
We did note several platform-specific variations in our data.
However, it corrects for platform specific variations (i.e. probe design, hybridization efficiencies etc).
Such information is then combined with platform-specific expression data.
Although the literature is scattered with platform-specific sample preparation procedures, there is a paucity of studies reporting the systematic evaluation of sample preparation across multiple platforms.
This empirically indicates high precision of microarray measurements, allowing successful identification of true transcript variation over platform-specific noise for many genes, even with low inter-sample variation.
Libraries of the required HLS-based functional blocks (FBs) are included together with the platform-specific information.
The sequence coverage along the genome shows slight variations between the different sequencing platforms, likely arising from platform-specific biases (for an example, [30]).
Subtype models depend on one particular "training" data set with its own platform-specific data structure.
Further, the larger platform-specific biases for small indels and structural variations also strengthened the argument for using both platforms for greater sequencing accuracy.
To test phenotypic variation between genotypes, the same platform-specific models to be described for the SNP-FT association analyses were fitted for each platform omitting the SNP and population structure fixed effects.
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