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As many microarray probes may map to the same gene, the average probe value per gene was calculated.
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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For example, while many microarray probe intensities overestimate gene expression levels by several orders of magnitude, SSMIs for nearly all probes much more closely match TPM values determined by RNA-Seq.
Many microarray chips contain probes that are annotated as 'non-protein coding', indicating that there might be some valuable expression data that we can also mine for information.
For many microarrays, the probe consists of cDNA or oligonucleotides spotted on a glass slide, and the target is fluorescent labelled cDNA (or cRNA).
Many microarray platforms include multiple probes for a subset of genes.
Many of the tobacco microarray probes are identified only by EST codes in the manufacturer's specifications.
In many microarray applications careful selection of probes to uniquely match target transcripts can be used to eliminate cross-hybridization biases.
As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.
However, there are many microarray applications where it is unavoidable for probes to share some sequence similarity to off-target transcripts.
Many microarray experiments provide expression values for a list of probes instead of genes.
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