Second, the genomic location of microarray probes from different platforms may measure signal from different sets of transcripts for a given gene.
Since one gene can be interrogated with several microarray probes, three different methods were used transform the microarray expression data to one value per gene; the mean of all probes, the median of all probes or the probe with the value closest to the RNA-seq data.
This "qualitative" approach – although problematic due to comparison of signal intensities of different microarray probes which have different hybridization efficiencies (see e.g. [10]) – underlined the prospects of a transcript-specific analysis, which were further studied on the quantitative level as follows.
We would like to note that for 1391 genes, mRNA decay rates were not consistent between different microarray probes (>2-fold difference).
cDNA microarray probes are two different kinds containing exon 23 or intron 4. The probes containing exon 23 detect all known isoform expressions except GABAB1j.
This is difficult to do with microarrays, because sequence-specific effects result in huge variations in binding affinity for different microarray probes and the signal associated with each probe cannot be considered a measure of relative abundance of different genes within a sample.
Since one gene can be represented by several microarray probes, we used three different methods to convert these to a single value that could be compared to the RNA-seq data (mean, median and best probe, see Materials and Methods for details).
However, the microRNA annotation version used for the microarray probe design was different among the five different microarray platforms in April 2008.
The microarray probes could not distinguish between different transcripts from a single gene, so relative expression values represented the combined expression of all transcripts from one gene rather than of one specific transcript.
The use of cross-species hybridization (CSH) to DNA microarrays, in which the target RNA and microarray probe are from different species, has increased in the past few years.
