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However, given that each new generation of tools takes several years to mature, it is most likely that sequencing and microarrays will continue to coexist.
As these sources of error are identified and eliminated, expression microarrays will continue to provide progressively more sensitive measures of gene expression.
However, many of the challenges that were present in measuring gene expression using microarrays will continue to be present in RNA-Seq experiments because they originate from biological rather than technical sources.
Until the processing time and cost of high throughput sequencing (including data analysis) decreases enough to be feasible for large numbers of samples at sufficient depth, microarrays will continue to be a valuable tool.
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Despite this improvement, overlap in expression results between identical genes on KRM2 and KRM1 is, as expected, not perfect, and microarray results will continue to be used, by our lab and others, as part of a discovery process requiring individual gene verification by methods such as RT-PCR.
Agilent Technologies will continue to license Rosetta's FlexJet microarray technology, which uses technology similar to that found in inkjet printers.
Microarray expression analysis has revolutionized many facets of biology and will continue to be applied widely.
The responses indicate that a lack of standardization will continue to represent a barrier to sharing microarray data and to the development of public databases.
Annotation of microarray platforms has improved greatly over the past several years, but errors in annotation will continue to affect analyses until genomes are completely validated and curated.
For these reasons, it would appear likely that qRT-PCR will continue to be used extensively for the validation of microarray expression data [ 15].
Undoubtedly, the trade-offs between call rate and call quality will continue to be an important issue surrounding the use of resequencing microarrays for mutational analysis.
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