For this study, we therefore decided that, as the percentage of tumour cells did not differ between samples with low and high numbers of CD8+ TILs, it was safe to assume that differences in non-lymphocyte-restricted genes and pathways reflected differences in gene expression by tumour cells.
We tested if distribution of allele frequencies differed between samples with first computing pairwise FST (according to [85]), and determining their statistical significance by 10,000 permutations with MSA 3.12 [86].
In the gene expression analysis, EVI1 expression differed between samples with gain versus without gain, exhibiting higher expression in the gain group.
The Significance Analysis of Microarrays (SAM) package was used to identify genes whose expression significantly differs between samples with a false discovery rate (FDR) of less than 5% [ 51].
Cortisol-corrected aldosterone concentrations (AC) differed greatly between samples with moderate and high Cadrenal/ Civc values.
Note that the agreement score depends on the nature of the tumour samples being rated, so, as for most studies of inter-rater agreement, comparison between studies with differing case-mixes of tumour samples requires care.
A straightforward interpretation of the data published thus far is complicated by the relatively small overlap between results obtained with differing analytical platforms, sample cohorts and bioinformatics methods [ 24].
From the result of HRBS measurement, In composition was differed between among the samples with different film thicknesses, and increased along the growth direction.
This results in 3860 cRNAs, where 1309 cRNAs are spiked in with differing concentrations between the S and C samples.
With regards to Lnn. mandibulares and tonsils, the number of samples with histopathological lesions, differed marginally between the two groups.
