Interesting comparison of arrays vs RNA-seq, maybe arrays are not so dead yet 
See Table 2 for interesting comparison of throughput in a clinical setting if expecting similar measurement precision (it would take 6-13X more time on a HiSeq and 100X-200X more time on the more ubiquitous GAII than to use an custom designed array)
Still sequencing will eventually catch up... give it another year..
Human transcriptome array for high-throughput clinical studies
A 6.9 million-feature oligonucleotide array of the human transcrip-
tome [Glue Grant human transcriptome (GG-H array)] has been
developed for high-throughput and cost-effective analyses in clin-
ical studies. This array allows comprehensive examination of gene
expression and genome-wide identification of alternative splicing
as well as detection of coding SNPs and noncoding transcripts. The
performance of the array was examined and compared with
mRNA sequencing (RNA-Seq) results over multiple independent
replicates of liver and muscle samples. Compared with RNA-Seq
of 46 million uniquely mappable reads per replicate, the GG-H
array is highly reproducible in estimating gene and exon abun-
dance. Although both platforms detect similar expression changes
at the gene level, the GG-H array is more sensitive at the exon
level. Deeper sequencing is required to adequately cover low-
abundance transcripts. The array has been implemented in a mul-
ticenter clinical program and has generated high-quality, repro-
ducible data. Considering the clinical trial requirements of cost,
sample availability, and throughput, the GG-H array has a wide
range of applications. An emerging approach for large-scale clini-
cal genomic studies is to first use RNA-Seq to the sufficient depth
for the discovery of transcriptome elements relevant to the dis-
ease process followed by high-throughput and reliable screening
of these elements on thousands of patient samples using custom-
designed arrays.
http://www.pnas.org/content/early/20....full.pdf+html
See Table 2 for interesting comparison of throughput in a clinical setting if expecting similar measurement precision (it would take 6-13X more time on a HiSeq and 100X-200X more time on the more ubiquitous GAII than to use an custom designed array)
Still sequencing will eventually catch up... give it another year..
Human transcriptome array for high-throughput clinical studies
A 6.9 million-feature oligonucleotide array of the human transcrip-
tome [Glue Grant human transcriptome (GG-H array)] has been
developed for high-throughput and cost-effective analyses in clin-
ical studies. This array allows comprehensive examination of gene
expression and genome-wide identification of alternative splicing
as well as detection of coding SNPs and noncoding transcripts. The
performance of the array was examined and compared with
mRNA sequencing (RNA-Seq) results over multiple independent
replicates of liver and muscle samples. Compared with RNA-Seq
of 46 million uniquely mappable reads per replicate, the GG-H
array is highly reproducible in estimating gene and exon abun-
dance. Although both platforms detect similar expression changes
at the gene level, the GG-H array is more sensitive at the exon
level. Deeper sequencing is required to adequately cover low-
abundance transcripts. The array has been implemented in a mul-
ticenter clinical program and has generated high-quality, repro-
ducible data. Considering the clinical trial requirements of cost,
sample availability, and throughput, the GG-H array has a wide
range of applications. An emerging approach for large-scale clini-
cal genomic studies is to first use RNA-Seq to the sufficient depth
for the discovery of transcriptome elements relevant to the dis-
ease process followed by high-throughput and reliable screening
of these elements on thousands of patient samples using custom-
designed arrays.
http://www.pnas.org/content/early/20....full.pdf+html