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Since each training data set was measured on a different microarray platform, there was no expectation that the signal for each data set would be directly comparable.
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Inherent to the microarray platforms, there are often multiple probesets or probes mapping to the same gene.
Furthermore, in all microarray platforms there were a number of genes that were detected as present but not found in the MPSS libraries.
Among the 97 such genes (UniGene IDs) common to all five microarray platforms, there were 11 that were found to be lacking the DpnII recognition site ("GATC") and could not be expected to give any signal in MPSS.
In terms of the microarray platforms used, there are insufficient differences to explain the reported discrepancies.
While microarray-based transcriptional analysis is a useful tool for functional genomics in fish, to date there has been no microarray platform available for catfish species.
There are advantages to each microarray platform.
The advantage of using a microarray platform to genotype a defined set of SNP loci for karyomapping is that there are no incidental findings at the sequence level.
Of these genes, there was an overlap of 29 genes with similar behavior in a second database using the same microarray platform.
With the relatively noisy measurements obtained from microarrays, there is the risk these modest changes in expression may fall within the error bounds of the microarray platform, and be biologically irrelevant.
Only platforms for which there are a notable number of publicly available expression data sets were included in this analysis, and therefore, microarray platform probe mapping was limited to 13 species (A.
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