There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.

deposited. In the 1980s the number of deposited structures began to increase dramatically. This was due to the improved technology for all aspects of the crystallographic process, the addition of structures determined by nuclear magnetic resonance (NMR) methods, and changes in the community views about data

to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward.

More than twelve years have elapsed since the first public release of WEKA. In that time, the software has been rewritten entirely from scratch, evolved substantially and now accompanies a text on data mining [35]. These days, WEKA enjoys widespread acceptance in both academia and business, has

The application of volume rendering techniques to the display of surfaces from sampled scalar functions of three spatial dimensions is explored. Fitting of geometric primitives to the sampled data is not required. Images are formed by directly shading each sample and projecting it onto

DBpedia is a community effort to extract structured information from Wikipedia and to make this information available on the Web. DBpedia allows you to ask sophisticated queries against datasets derived from Wikipedia and to link other datasets on the Web to Wikipedia data. We describe

, on-line groups are becoming increasingly prominent due to the growth of community and social networking sites such as MySpace and LiveJournal. However, the challenge of collecting and analyzing large-scale timeresolved data on social groups and communities has left most basic questions about

Data analysis plays an indispensable role for understanding various phenomena. Cluster analysis, primitive exploration with little or no prior knowledge, consists of research developed across a wide variety of communities. The diversity, on one hand, equips us with many tools. On the other hand

We collected a corpus of parallel text in 11 languages from the proceedings of the European Parliament, which are published on the web 1. This corpus has found widespread use in the NLP community. Here, we focus on its acquisition and its application as training data for statistical machine

The explosion of image data on the Internet has the potential to foster more sophisticated and robust models and algorithms to index, retrieve, organize and interact with images and multimedia data. But exactly how such data can be harnessed and organized remains a critical problem. We introduce