The major shortcomings of the present work are the experimental cDNA microarray methodology and the small sample size with relatively short follow-up time.
Using this approach not only can mRNA levels be validated, but also differences in microarray methodology, normalization and data processing methods.
Other studies have used similar numbers of proteins for comparison of ICAT and mRNA microarray methodologies (N = 245, 289, 425) [3]–[5].
In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes.
Co-regulation of DBI with lipid metabolism is found consistently in experiments representing the two current microarray methodologies, Affymetrix oligonucleotide arrays [ 21] and spotted two-color cDNA arrays [ 22] (Table 1).
Several power calculations for microarray methodologies exist, consequently sample size was determined and compared with two power calculation approaches.
Thus, we propose that peptide microarray methodologies are a powerful new tool for elucidating molecular interactions at chromatin.
The heterogeneity between ducts of the same patient that was revealed in this study provides a cautionary note for interpretation of data from microdissection or microarray methodologies in which a small number of samples each with only a few cells are used to characterize a tumor, since the heterogeneity of a tumor in vivo may not be reflected in such small samples [ 24, 25].
The heterogeneity between ducts that was revealed in this study provides a cautionary note for interpretation of data from microdissection or microarray methodologies in which a small number of samples with only a few cells are used to characterize a tumor, since the heterogeneity of a tumor in vivo may not be reflected in such small samples [ 24, 25].
These observations are consistent with previous reports of gene expression profiling using microarray methodology [ 36], and provide validation of the RT-PCR assays.
