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Trouble Shooting

Problems running ChIPOTle

1. Make sure all inputed columns contain the right data types. Array spot names - strings or numbers, Chromosome or region ID - strings or numbers, Start cord - whole number, Stop cord - whole number larger then Start cord.

2. Make sure the worksheet that you are running the program from does not contain any sheets except the sheet containing your data.

Problems with the Results

1. There are a few or zero significant peaks. Make sure that your data is Gaussian and correctly centered. Look at the section in the user guide "Is my data Gaussian?". If your data is Gaussian and correctly centered, there are many possible causes. 1) What is the resolution of your array compared to the shear size? If the resolution of your array is larger then your shear size there may not be a neighbor affect in your experiments. Try using the permutation simulation approach, it is less affected by the number of arrayed elements per peak. 2) If you are using an average or median from many replicates make sure that the replicates can be combined accurately. If the replicates have differing variances then straight average or median would not be approprate. Try a weighted average before running ChIPOTle.

2. There are lot of Significant Negative Regions. Try increasing the p-value and make sure that you data does not contain a left skew. This skew could be caused by a biological aspect of the data. If your data does contain a heavy left skew you may need to try the permutation simulation approach.