Instead of taking the ratios of promoter-scores between the input and ChIP DNA, we compared the promoter-scores and the FDR of the input and ChIP channels as independent entities (see Additional file 3).
With each method, we calculated a distance matrix for the input sequences, and we compared this matrix to a reference distance matrix that we calculated with the program Dnadist from the PHYLIP package [ 49] based on a reference multiple alignment.
For Caco-2 CLIP samples with input RNA as control, we compared four different ranking and normalization strategies, including Raw, AVE-CLIP, AVE-INPUT, and INPUT (Materials and Methods).
To test whether reliability weighting allows ICx neurons to integrate coherent inputs in each frequency channel, we compared the average interaural correlation across locations of concurrent sounds with the IPD reliability.
We compared the inputs of dopamine neurons defined by eight major targets: different parts of the striatum (ventral striatum [VS], dorsal striatum [DS], tail of the striatum [TS]), cortex (mPFC, orbitofrontal cortex [OFC]), central amygdala (Amy), globus pallidus (GP), and lateral habenula (lHb).
To quantify the differences between inputs to dopamine neurons with different projection sites, we compared the percentage of input neurons observed in each brain area in each condition.
We compared the input parameters V sw, logP nV 2, and logP B with the output parameter logP G12, logP TNB, and logP AQU.
To assess how the amount of input RNA affects microarray results, we compared intensities found using 5 versus 100 ng of murine liver RNA (Experiment 2).
First, we compared how many inputs each population receives from the nucleus that it projects to.
Moreover, we estimate the uncertainty associated to each input variable and we compare it to the overall one.
