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GeneChips were normalized using the median signal across all 72 microarrays.
All data points were median scaled to 1 using the median signal intensity value for data points labeled as present.
Technical replicate probes were averaged using the median signal intensity.
Differential expression was assessed using LIMMA and EBarrays [ 45, 46] using the median signal of probes representing genes.
Using the median signal values, the HpaII/ MspI ratio is then calculated for each CCGG segment and converted to a log2 value to obtain the M-value.
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We used the median signal intensities of the interior probes as an indicator of the expression level of each gene.
For each time point, the fluorescent signals for each probe were normalized using the median fluorescent signals of the corresponding microarray and scaled using the mean DNA content estimated by flow cytometry for the corresponding time point (see Materials and Methods and supplementary fig. S0, Supplementary Material online).
For each time point, the fluorescent signals for each probe (F635 and F532) were normalized using the median fluorescent signals of the corresponding microarray and scaled using the mean DNA content N for the corresponding time point.
For the first method, the reference is computed by using the median of the signals of the samples labeled as normal for each SNP.
Following the method of Shyu et al. [31], BiFC specificity was determined using the median of the CFP/RFP signal for each condition.
We have tried to overcome this by using the median frequency of the audio signal to provide a measure which is independent of signal power and can exploit the characteristic high frequency components of the cough sound.
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