The differences between the different samples (replicates) were counted and divided by the total number of phenotypic comparisons to get the error rate (calculated according to Bonin et al. [ 49]).
The differences between the different samples were analysed using one-way analysis of variance (ANOVA) followed by Tukey's honestly significant difference post hoc test with α = 0.05, coupled with Welch's statistic.
However, due to the non-saturated nature of our EST databases and the relatively short average unigene length derived from pyrosequencing, these specific sequences cannot be a reliable representation of the transcriptional differences between the different samples.
Stromal macrophages and lymphocytes served as internal control for BNIP3 expression, as they showed a similar strong mRNA expression in all slides, as confirmed by immunohydrido double staining for CD68 respectively CD3 (data not shown), whereas tumor BNIP3 signal intensity differed between the different samples.
This is due to the fact that the content of pores over 0.5 μm is practically the same in SCC and NVC, but for smaller pore sizes, which are therefore only accessed when water under pressure is applied, the differences in porosity between the different samples is more pronounced.
As the mAs determines the number of incident photons, in X-ray diagnostics machines, the mAs is reduced when the energy (keV) is too high (this is the case when 40 keV is applied), not only to protect the X-ray filament but also obtaining less differences in the GSI between the different samples.
There was no apparent difference in cell size between the different samples of the sugar beet tap-root cells but that cell walls thickened during development.
To control for differences in allele frequency between the different samples, data from the human genome diversity project (22) were used.
Variation in the ThT fluorescence signal between the different samples may be attributable to stochastic sampling effects or possibly to a heterogeneous population of abnormal alpha-synuclein species in the homogenates.
Interestingly, while we found no marked difference in gene expression between the different samples (see below) histopathological staining showed a distinctive membranous pattern in the metastatic samples, while primary and local recurrences showed both membrane and cytosolic staining (see Figure 1A C).
As an expression measure, RPKM was used in an effort to normalise for the differences in the numbers of mapped reads between the different samples.
