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For this purpose, our study was conducted with Ankara as the capital of Turkey and with more sample groups.
We envision this tool will be particularly useful for assessment of raw data quality following the identification of microarray features that were differentially expressed in a statistical comparison of two or more sample groups.
However, once considering 4 or more sample groups for comparison, labeling methods were recommended as more time saving approaches.
One can determine the relative inclusion or skipping rate of an exon between two or more sample groups (differential splicing) using both metrics together.
Three and more sample groups were analyzed with a Kruskal Wallis test followed by Dunn's posttest comparing each sample group with the control group.
Thus, these potentially interesting peaks can be subjected to further statistical analyses in MeltDB and become accessible for profiling experiments, where the aim is in general to find differences in the metabolic composition of two or more sample groups.
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In particular, the mouse data showed significantly higher correlations among replicate samples than the human data (Wilcoxon test, P < 0.01), suggesting that they constituted more homogeneous sample groups (Supplementary Figure S3).
Further investigations will be necessary to verify the association of other ATM SNPs in more representative sample groups in order to establish whether single nucleotide polymorphisms or gene haplotypes may actually contribute to the toxicity of normal tissue.
In all the datasets, class 2 represents a more malignant sample group than class 1.
Our conclusions are thus limited and in need of replication with a larger, more diverse sample group.
To test whether the predictions would be improved in a more homogeneous sample group, we stratified the samples into 55 ER-positive and 17 ER-negative pairs.
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