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On most common microarray platforms many genes are represented by multiple probes.
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This is due to the lack of microarray platforms for many S. cerevisiae strains and non-Saccharomyces species.
As is the case for many microarray platforms, we found that proper oligonucleotide design is critical.
Many microarray platforms include multiple probes for a subset of genes.
Over the past years, many microarray platforms, based on different technologies, have been developed by commercial and academic institutions.
Although we have identified spatial biases by their manifestation in the form of periodic autocorrelation, which in itself depends on microarray design, their frequency of occurrence should be constant over many microarray platforms irrespective of design.
Several of these studies have been very comprehensive encompassing many microarray platforms analyzed in both one and two colors, employing different probe types spotted both in-house and commercially, and using data from the same samples analyzed in several different laboratories.
Recently, its advantages over microarray platforms have been described by many comparative reports [ 16].
The Ensembl database (Hubbard et al. 2009) maintains and regularly updates a list of probeset mappings for many popular microarray platforms.
Identifying the source of variability between the different microarray platforms was not straightforward since many factors could have influenced the expression data.
First, all publically available datasets from immune response experiments using many different microarray platforms and pathogens (Additional file 1: Table S1), including the ones for the response to PRRSV, were considered for the first global meta-analysis.
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