This paper is about how to control the quality of microarray expression data. Since gene-expression microarrays have become almost as widely used as measurement tools in biological research, we survey microarray experimental data to see possibilities and problems to control microarray expression data. We use both variable measure and attribute measure to visualize microarray expression data. Ac...

Identification of a reference gene unaffected by the experimental conditions is obligatory for accurate measurement of gene expression through relative quantification. Most existing methods directly analyze variability in crossing point (Cp) values of reference genes and fail to account for template-independent factors that affect Cp values in their estimates. We describe the use of three simpl...

The condensation of nucleosome arrays into higher-order secondary and tertiary chromatin structures likely involves long-range internucleosomal interactions mediated by the core histone tail domains. We have characterized interarray interactions mediated by the H4 tail domain, known to play a predominant role in the formation of such structures. We find that the N-terminal end of the H4 tail me...

Here we illustrate several uses of the package gaga, including simulation, differential expression analysis, class prediction and sample size calculations. In Section 1 we review the GaGa and MiGaGa models. In Section 2 we simulate gene expression data, which we use to fit the GaGa model in Section 3. Diagnostics for model goodness-of-fit are presented in Section 4. Section 5 shows how to find ...

INTRODUCTION Spectral-domain optical coherence tomography findings in a patient with acute macular neuroretinopathy, and correlation with functional defects on microperimetry, are presented. CASE PRESENTATION A 25-year old Caucasian woman presented with bitemporal field defects following an upper respiratory tract infection. Her visual acuity was 20/20 in both eyes and a dilated fundus examin...

Abs t rac t . In [3] a general fohl ol)eration has been introduced for definite programs wrt computed answer substitution semantics. It differs from the fold operation defined by Tama.ki and Sato in [26,25] because its application does not depend on the tra.~sformation history. This paper extends the results in [3] by giving a more powerful sufficient condition for the preservation of computed ...

We consider array experiments that compare expression levels of a high number of genes in two cell lines with few repetitions and with no subject effect. We develop a statistical model that illustrates under which assumptions thresholding is optimal in the analysis of such microarray data. The results of our model explain the success of the empirical rule of two-fold change. We illustrate a thr...