### This is a sample configuration file for data from platforms ## other than Affymetrix. Users must prepare a single text file (without column headers) ## to include all informations. The first two columns need to be ## chromosome and positions of the probes. From the third column ## are probe signals (log ratios). [data] Title=Agilent_test Format=text ## using text file (instead of CEL and BPMAP) as inputs ## location of the file file=/dir/to/file/ChIP-chip.txt ## Working folder. Both temporary and final results will be written to this folder. WorkFolder=. ## The column numbers for conditions. The following examples mean ## columns 3 and 4 are for cond1 condition, 5 and 6 are for cond2 and so on. [Condition] cond1=3 4 cond2=5 6 cond3=7 8 ## Parameters for peak finding. [peak finding] ## Length of a potential binding region. candidateLength=1000 ## Allowable peak length with in the potential binding regions. bumpLength=300 500 700 900 ## Maximum gap allowed in a peak. maxGap=300 ## Minimum number of probes allowed for a peak. MinProbe=6 ## FDR cutoff values for defining a peak list. FDRcutoff=0.2 ## Method to compute FDR for a peak list. ## FDR=0: compute from posterior probabilities (faster and recommended); ## FDR=1: empirically estimate from data using negative intensities. computeFDR=0