The current existing literature offers little guidance on how to decide which method to use to analyze one-channel microarray measurements when dealing with large, grouped samples. Most previous methods have focused on two-channel data;therefore they can not be easily applied to one-channel microarray data. Thus, a more reliable method is required to determine an appropriate combination of individual basic processing steps for a given dataset in order to improve the validity of onechannel expression data analysis. We address key issues in evaluating the effectiveness of basic statistical processing steps of microarray data that can affect the final outcome of gene expression analysis without focusingon the intrinsic data underlying biological interpretation.
Analysis of Variance ; Dataset ; Gene Expression ; Statistics as Topic

Brain edema, the infiltration and accumulation of excess fluid causing an increase in brain tissue volume, often leads to a rise in intracranial pressure (ICP) and is a key contributor to the morbidity and mortality associated with brain injury. We examined the mechanisms for vasogenic brain edema produced by focal cerebral ischemia. To test the mechanisms underlying vasogenic brain edema, we compared the expression of endothelial nitric oxide synthase (eNOS) and aquaporin-4 (AQP4) in the penumbra of brain tissues after focal cerebral ischemia. The expression of eNOS and AQP4 in the ischemic penumbra was determined by quantitative immunoblot analysis. In focal cerebral ischemia, eNOS expression increased significantly to 129%+/-6% of the value for sham-operated controls (n=4, P<0.01). In contrast, AQP4 expression decreased significantly to 52%+/-3% of the value for shamoperated controls (n=4, P<0.01). These findings suggest that the expression of eNOS and AQP4 in the focal cerebral ischemia may play different roles in the formation of vasogenic brain edema. Additionally, a larger decrease in the neuronal nuclei (NeuN) (39%+/-7% of the value in sham-operated controls; n=4, P<0.01) than the decrease in glial fibrillary acidic protein (GFAP) (53%+/-14% of sham-operated controls; n=4, P<0.01) in the penumbra after focal cerebral ischemia suggests that the neurons are more susceptible to ischemic injury than are the astrocytes.
Astrocytes ; Brain ; Brain Edema ; Brain Injuries ; Brain Ischemia ; Edema ; Glial Fibrillary Acidic Protein ; Intracranial Pressure ; Neurons ; Nitric Oxide Synthase Type III