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Since the distributions defied further standard methods of normalisation to allow comparisons (square root, natural log and reciprocal), regressions, ANOVAs and t-tests were ruled out.
Mean normalisation was previously shown to outperform other methods of normalisation in terms of better reduction of technical variation and more accurate appreciation of biological changes [ 25].
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This spike-in method of normalisation was chosen because the frequently used sno normalisers are not expressed in cMVs.
While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control.
This discrepancy may be a result of different patient populations and different methods for normalisation of mRNA expression.
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.
Thus, RNM provides an effective method for normalisation of gene expression data obtained from DNA microarrays.
We used Li and Wong's invariant set method for normalisation of the data sets (Li and Hung Wong, 2001).
However, analysing FFPE samples holds the advantage of a large-scale biomarker validation using a generally accepted method, although a validated method for normalisation of data in this setting is still warranted.
The aim of the present study was therefore to use this approach combined with unique in-house developed method for normalisation of DGGE data to investigate how bacterial populations differed between healthy people and those with UC and IBS and identify the bacterial species which are responsible for these differences.
Here we present a method for designing tiling arrays and methods for normalisation, background estimates/adjustments and data analysis of tiling experiments.
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