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POTION first tries to calculate q-values using the qvalue method as described in [ 25] and implemented in Statistics:Multtest Perl module, estimating the proportion of true null hypotheses using a bootstrap procedure.
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Quantitative measures of covariance have been implemented in χ2 statistics and mutual information.
Correlations between fMRI and MEG data were explored using Spearman's correlation, implemented in SPSS Statistics 20.
PE values were non-normally distributed and so were compared between genotype groups using a Mann–Whitney U test, implemented in SPSS Statistics 20 (IBM, Armonk, NY).
Since this sample contained missing data many participants would be lost from the ANOVA analysis that could be implemented in standard statistics packages such as SPSS.
Here we have applied robust regression based on Huber's error function as it is implemented in the statistics software R in the rlm-method in the package MASS.
The DMR finder algorithm was implemented in R statistics and the script is available in Additional file 4. The DMR finder can be used for 450k data (using Illumina CpG identifiers) as well for other types of DNA methylation data (using genomic locations).
The Pearson's partial correlation coefficient between the mean BOLD signal time-series within the left and right peri-rolandic regions was then calculated controlling for the whole-brain mean signal and the 6 detected head motion parameters, using tools implemented in the statistics toolbox of Matlab (The Mathworks, Natick, MA, USA).
Robust Multi-Array Average (RMA) expression measurement was also used with the help of probe sequence (GC content) information (GCRMA) [37] as implemented in BioConductor R statistics (www.bioconductor.org).
The resulting data was summarized using custom scripts implemented in the R statistics package [ 49].
Correlation p-values and regression lines were computed using the linear model function implemented in the R statistics package.
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