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Additional file 5 is a supplementary figure showing that certain highly-expressed microarray probes do not accurately measure gene expression.
Moreover, several 4q35 genes display very close homologues on other chromosomes and, as reported elsewhere (23, 24), microarray probes do not target specifically their 4q35 copy.
Earlier reports have shown that, many microarray probes do not have 100percentt identity, along their entire length, to any transcript [ 25].
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What will the probes do?
Jetset: Selecting the optimal microarray probe set to represent a gene.
Interestingly, when microarray probing was done in 100 mM KCl/10 mM MgCl2 instead of 300 mM KCl/10 mM MgCl2, no detectable binding was observed.
Additional file 7 is a supplementary figure showing that quality control and scaling of microarray probes can be done well with as few as 16 matched RNA-Seq samples.
Some published SHA and FISH probes did not work in a microarray format.
To avoid biases in estimation of genome-wide correlation between two profiles, we first excluded genomic regions that did not contain microarray probes and had high variability in INPUT-seq variability.
The microarray probes used in the studies in Oncomine do not distinguish between neonatal and adult SCN5A splice variants.
Microarray probes were matched to gene identifiers using the CDF array annotation (version 18) provided by the University of Michigan microarray© lab56.
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