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First we calculated the c.f. between our skin GET and the 56 gene expressions from each array of the dataset GSE6932 [ 23] where NHEK epidermal progenitor cells had been treated with 2- 3,4,5-trimethoxyphenylamino -pyrrolo[2,3-d]pyrimidine (PP-2- 3,4,5-trimethoxyphenylamino -pyrrolo[2,3-d]pyrimidine
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To eliminate correlations based on noisy expression, we only considered probe sets which have a log2 expression signal >6 in at least one array of the entire dataset.
The input MS2 spectrum data are parsed into the numpy arrays through the iteration of the dataset.
The remaining 483 sets of array data were processed using Robust Multi-array Average (RMA) separately for each of the 3 array types in the dataset.
We would like to thank the curators of The Arabidopsis Information Resource (TAIR) for helpful suggestions for tracking the experimental conditions of most of the micro-arrays in the dataset.
This result is not unexpected, as the single reference design of most CGH arrays constricts the dataset in such a way that discards information that would resolve irregular distances.
This series reflects the most complete version of the dataset (46 arrays, as used in Additional file 4).
The results from experiments carried out on an array of datasets showed that the incorporation of the GO DAG structure leads to more accurate predictions.
One reason for these differences is the wide array of datasets used in the analyses.
Normalization of imputed dataset: imputed dataset was normalized using quantile normalization in R (Bolstad et al., 2003 ) and logged to base 2. Array outlier detection: dissimilarity matrices of the normalized dataset were generated in AVADIS-Pride (Gwadry et al., 2005 ) to determine outlier arrays within the dataset.
For the 'P/M' set, only those genes were included that had 'P' and/or 'M' calls in at least 50% of the arrays of each dataset (n = 8 to 16).
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