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The marker set was filtered according to pair-wise LD (r2 cut-off = 0.2) in order to remove correlated markers.
Two analyses were performed to assess whether LD affected the linkage results from our data, each using a different approach to exclude SNPs in order to remove correlated markers.
In fact it is often better to reduce the number of restraints and apply constraints instead, which remove correlated parameters where possible.
Using the untreated eye as a control is thought to remove correlated variability due to diurnal fluctuation [ 1, 4], operator technique, tonometer calibration, etc.
A principal component analysis (PCA) was carried out on the 19 BIOCLIM variables in the WorldClim data set [ 30] to remove correlated variables, since these can lead to overfitting of the model.
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We found that, if we removed correlated variables prior to model selection, the final models were artefacts of the variables we had selected.
It is likely that when individual activity annotations are removed, correlated values from similar assays remain in the data set and are the reason that the loss in performance is not linear.
We tested this model (Model 3 - 1-factor, item 1 removed, correlated error between items 3 and 4).
However, the blood cultivation data from these seven patients before the catheters were removed correlated with DGGE results in catheter number 3 and 11, but not number 6, 10 and 12.
The patterns of association will be reviewed by the study team to remove highly correlated redundant variables, or replace highly correlated factors with averages or first principal component scores.
To avoid convergence problems during parameter estimation, we applied principal component analysis (PCA) to the 14 different environment variables (both from the VEMAP and CRU05 data) to remove highly correlated variables.
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