These discrepancies might be related to the use of different microarray platforms with different normalisation methods and differences in the degree of contamination by non-neoplastic cells in specimens, or heterogeneity in the patient population undergoing study (Konstantinopoulos et al, 2008).
Here we report the first comparative analyses of multiple gene transcription data sets obtained in parallel with different microarray technologies over several popular normalisation methods using multiple cross-platform concordance criteria.
While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control.
When qRT-PCR data derived in rats for a small election of genes were used to assess the effects of normalisation methods on microarray-based gene expression data, we found that for Affymetrix, MAS 5.0, RMA, GC-RMA and the Li-Wong method all had very high correlations with the logarithm of the qRT-PCR fold change, and the highest was comparison-dependent (see Additional file 9).
Recently, other normalisation methods have been proposed that adapt methods originally developed for microarrays and other high-throughput genomic technologies [ 19- 21].
Location normalisation methods like LoWeSS are used to (non-linearly) normalise log ratios within an array, additional methods for normalisation of scale are used to compare log-ratios across multiple arrays.
The results of our study showed that RNM greatly reduced the variances within slides and between slides, performing better than any other studied normalisation methods, increasing the CCR by 17% and greatly improving the effective reproducibility of microarray data.
An investigation has been conducted to evaluate the performance of normalisation methods for the uniaxial bias extension test.
Evaluation of the normalisation methods applied has been carried out using four different criteria.
For completeness both normalisation methods have been applied to all data for comparison.
