BackgroundSimultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the combination and comparison of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, software for the selected method must be obtained and incorporated into a data analysis workflow.ResultsUsing two publicly available cross-platform testing data sets, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data. Scatter and ROC-like plots are produced and new statistics based on those plots are introduced to measure the effectiveness of each method. Bootstrapping is employed to obtain distributions for those statistics. The consistency of platform effects across studies is explored theoretically and with respect to the testing data sets.ConclusionsOur comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. We provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. The package can be downloaded at http://alborz.sdsu.edu/conor and is available from CRAN.
Though it has become conventionalto refer to the “new cosmopolitanisms” when discussing the resurgence of the term in the 1990s, current debates about cosmopolitanism can be traced back to its usages in the nineteenth century. In both its Victorian and contemporary contexts,cosmopolitanismranges in connotation from the pejorative to the progressive and in denotation from a phenomenon to an ideal. This constitutive ambivalence helps to explain the controversy that has attended the term, both then and now.
Victorian emigrant ships headed to the Australian colonies carried printing presses and published newspapers on board for the entertainment of passengers; the emigrants themselves generated most of the content. Based on archival work in Australia, South Africa, and England, this essay analyzes poetry published in these ship newspapers, and shows how emigrant poems engage both nostalgically and parodically with canonic poetry of the period: works by Alfred, Lord Tennyson, Henry Wadsworth Longfellow, and Thomas Hood. Shipboard emigrant poems showcase the process of transition from home to abroad, British citizen to colonial subject; they offer an important view into the culture of Victorian emigration and colonialism.
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