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Ratio results from control vs. infected replicates were combined using the default ratio experiment builder.
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Initially, using the default parameters reported, the calculated ratio of the number of patients with severe (grade 3 4) neutropenia to that without any hematopoietic toxicity in the control group was 1.71, which differed considerably from the reported value of 0.0968 (data not shown).
Scaled gene expression values for pretreatment, post-treatment (10 μ M MP for 24 hours) and fold-change (post-treatment vs pretreatment ratio) were calculated using the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0) (Cheok et al, 2003).
Two-channel normalization was performed to adjust the centre and spread of the distribution of intensity log-ratios [ 61] using the default method of the "marray" package [ 62] in Bioconductor version 1.8 [ 63].
The peak shift Δδ was set by using the default parameters of the software package and signal-to-noise ratio (S/N) was set to 100.
Individual-based CNV calling was performed using the default parameters of the HMM model by integrating Log R Ratio, BAF, population allele frequency and the SNP distance.
We use the Canny[31] edge detector as implemented in MATLAB using the default σ = 2 and the default high to low threshold ratio of 40%. .
One way Hierarchical clustering of the ratios (Control vs. Stress) of significantly differentially expressed genes were performed in JMP Genomics using the default settings of ten clusters.
The second keep using the default value of.
Ordering was performed using the default parameters.
MATCH was executed using the default settings.
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