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This procedure was repeated for each sample, computing the statistical significance of each gene in the various leave-one-out datasets.
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Sample computed results are presented.
For every bin, the per-million reads coverage of each sample was normalized using the size factor of the sample computed by DESeq [ 57], and replicates were averaged.
To summarize the overall composition, we then for each sample computed the mean membership probability across all individuals to the different clusters.
In the cases that we studied, this procedure increased the computational time of each sample by a factor of 5 when compared with a sample computed using the standard Monte Carlo.
The protector aligns these L samples with the first L received samples, computes the correlation, shifts the alignment by one sample and then re-computes the correlation.
In the above formula, the numerator is an averaged value of three cross-correlation samples computed between four consecutive sample blocks of length each.
Scaling factor values for all 223 samples computed at a target intensity value of 500 were examined.
The second method (MHS: median of HapMap samples) computes the reference using the median of external control samples (in this case they are from HapMap).
Genes with similar expression patterns were grouped as hierarchical clusters with distances between samples computed using Pearson correlations for similarity measures and average linkage as the clustering algorithm.
Baseline investigations consist of blood tests, an oesophagogastroduodenoscopy with tumour biopsy samples, computed tomography (CT) of the chest and abdomen, renography, cardiac ejection-fraction scan, electrocardiography, and when the preoperative CT-scan suggests peritoneal carcinomatosis, diagnostic laparoscopy.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com