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Taking the residuals after median smoothing (window size 110 011 bp) removed this trend.
We chose a 6 kb cutoff because the Lowess smoothing window size of our microarray data was set at 6 kb.
The model selection method is sensitive to the smoothing window size of G′-test in two ways.
Various distances between the two QTL were simulated to determine the probability of two QTL merging into one when their distance was smaller than the smoothing window size.
The LOWESS fitting is performed with a smoothing window size determined for each dataset as that which produces the least error between the fit and the raw data.
We then applied TEX-QTL on a chromosome with two QTL using 36 cM as the smoothing window size, chosen based on the results of the 1-QTL simulations mentioned previously.
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To investigate the effect of G′-test's smoothing window sizes on the number of false-positive and false-negative peaks, we simulated TEX-QTL on a chromosome with one QTL by using a range of smoothing window sizes.
The tested smoothing window sizes were 16, 20, 24, 28, 32, and 36 cM.
With an outside sliding-window and a masking-window size of 17, the CLCLpred model was further tested according to different smoothing window sizes.
To estimate the probability of identifying false peaks using different smoothing window sizes, we simulated a single QTL flanked by 50 cM on both sides.
The raw G-frequencies were smoothed (blue curve in Fig. 2), using the loess local regression method [ 20], and smoothing windows of size 50 nt or 100 nt, prior to analyzing the intron-G-frequency association.
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