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However this approach can be considered as limited in that it assumes that gene lists generated on the full dataset are correct; besides it is fastidious to implement and extremely time consuming.
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Image distortions and motion artifacts in the DTI dataset were corrected by applying affine alignment of each diffusion-weighted image to the b = 0 image, using FMRIB's Diffusion Toolbox (FSL, version 3.3; www.fmrib.ox.ac.uk/fsl).ac.uk/fsl
Preprocessing: Each 10-minute resting FMRI dataset was corrected for head motion using FLIRT FMRIBB's Linear Image Registration Tool [53]. Temporal drift was removed using a highpass filter of full width 200 s. The mean (over time) image was brain-extracted using BET [54].
With these findings in mind, all peaks predicted by Splitter in our own dataset were corrected by adding 200 bp to the 3' end, widening the peak.
Eddy current distortions and motion artifacts in the DTI dataset were corrected by applying affine alignment of each diffusion-weighted image to the b = 0 image, using FMRIB's Diffusion Toolbox (FSL, version 3.3; http://www.fmrib.ox.ac.uk/fsl).ac.uk/fsl
Having estimated interception α ^ j k and slope β ^ j k on the basis of control group, the whole dataset is corrected as follows: Y i j k C = Y i j k − Y ^ i j k = Y i j k − (α ^ j k + β ^ j k R i j k ).
All datasets were corrected for MR field inhomogeneity using SPM12 (http://www.fil.ion.ucl.ac.uk/spm) bias correction function with very light regularization.
All datasets were corrected for radioactive decay.
Non-biological experimental variation between the in vitro arrays and the sarcoma datasets was corrected using a previously described batch effect adjustment algorithm [36].
Non-biological experimental variation between the experimental system arrays and the ovarian cancer datasets was corrected using a previously described batch effect adjustment algorithm, ComBat (http://statistics.byu.edu/johnson/ComBat) [18].
Non-biological experimental variation between datasets was corrected using the batch effect adjustment algorithm as above.
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