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Table 3 List of sensors dan feature values No. Name of probes Value 1 Value 2 Value 3 1.
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Having 5 to 6 probes per gene, each gene signal ratio was given by the median of the corresponding probes values.
For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.
Segments were called gains or losses if their mean value exceeded 1.5 standard deviations from the mean probe value.
This is a modeling strategy that converts the perfect match probe value into an expression value for each gene.
No normalization was used in clustering, but for visualization purposes, the intensities were median-centered so that green represents values below the median probe value and red above.
A relative probe value of <0.7 indicates a monosomy, whereas a relative probe value of >1.3 indicates a trisomy.
Probe-values were log2-transformed, and samples were quantile normalized and hospital-adjusted by subtracting from each probe value the median probe value among samples from the same hospital.
The calculated background level for each sample is then subtracted from the adjusted probe value.
As many microarray probes may map to the same gene, the average probe value per gene was calculated.
For each contig and singleton with more than one probe, we tested the median probe value against this threshold.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com