PMC:2644708 / 53709-55769
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{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/2644708","sourcedb":"PMC","sourceid":"2644708","source_url":"http://www.ncbi.nlm.nih.gov/pmc/2644708","text":"Data simulation study\nGRSN was evaluated using simulated data produced by adding simulated gene expression and simulated non-linear artifacts (skew) to a cell culture dataset containing 10 replicated controls [14]. The 10 samples were first processed using the RMA method. Next, all possible permutations for dividing these 10 replicate samples into two groups of 5 (set A and set B) were calculated. Out of the 252 possible permutations, we randomly selected 100, thus ensuring that we had 100 randomly selected, yet distinct partitions of the original data. For each of these 100 distinct partitions (hereafter called a simulation), we added simulated Fold Change (FC) by applying a multiplication factor to selected transcripts (genes) in all samples in set B. For each simulation, we randomly selected 2500 genes. The first 1000 (out of the 2500 selected) were multiplied by +1.5 to simulate a FC of 1.5 up. A factor of +2 was applied to the next 500, a factor of +4 to the next 300, a factor of +8 to the next 200, a factor of 2/3 to the next 200, a factor of 1/2 to the next 200, and a factor of 1/4 to the final 100 genes. Thus, up regulation with FC in the range of 1.5 to 8 was simulated for 2000 genes and down regulation with FC in the range of -1.5 to -4 was simulated in 500 genes. The next step in each simulation was to add distinct, randomly generated skew to each sample. This was done by randomly generating curves similar to the calibration curves produced by GRSN when normalizing RMA processed data and using these as \"calibration curves\" to add intensity-dependent skew to the simulated samples. The final step in each simulation was to apply GRSN to correct the introduced skew. The simulated data was analyzed at each of the three stages in the simulation process just described, 1) after simulated FC was introduced, 2) after simulated skew was added, and 3) after GRSN was applied to correct the simulated skew. The results of these analyses were tabulated and/or averaged over all 100 simulations and reported in the results section.","divisions":[{"label":"Title","span":{"begin":0,"end":21}}],"tracks":[{"project":"2_test","denotations":[{"id":"19055840-16646809-8161631","span":{"begin":210,"end":212},"obj":"16646809"}],"attributes":[{"subj":"19055840-16646809-8161631","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecd493","default":true}]}]}}