FGX: a frequentist gene expression index for Affymetrix arrays

We consider a new frequentist gene expression index for Affymetrix oligonucleotide DNA arrays, using a similar probe intensity model as suggested by Hein and others (2005), called the Bayesian gene expression index (BGX). According to this model, the perfect match and mismatch values are assumed to be correlated as a result of sharing a common gene expression signal. Rather than a Bayesian approach, we develop a maximum likelihood algorithm for estimating the underlying common signal. In this way, estimation is explicit and much faster than the BGX implementation. The observed Fisher information matrix, rather than a posterior credibility interval, gives an idea of the accuracy of the estimators. We evaluate our method using benchmark spike-in data sets from Affymetrix and GeneLogic by analyzing the relationship between estimated signal and concentration, i.e. true signal, and compare our results with other commonly used methods.


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Time series often contain observations of several variables and multivariate time series models are used to represent the relationship between these variables. There are many studies on vector autoregressive moving average (VARMA) models, but the representation of multiplicative seasonal VARMA models has not been seriously studied. In a multiplicative vector model, such as a seasonal VARMA model, the representation is not unique because of the noncommutative property of matrix multiplication. In this articl...
Citation Formats
V. Purutçuoğlu Gazi, “FGX: a frequentist gene expression index for Affymetrix arrays,” BIOSTATISTICS, pp. 433–437, 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/38608.