On Mon, Aug 17, 2009 at 3:01 PM, Abhishek Pratap <abhishek.vit@gmail.com>wrote:

> Hi Sean
>
> Thanks for your suggestion on both the mailing lists. I am now reading
> the coverage values from a file and storing them as a data.frame and
> then creating a new numeric vector for each lane. Each vector may have
> 15000-45000 entries.  The values are integers with a significant
> difference in values, some could be between 0-1 eg (0.45,0.89) and
> then I also have values in range like  (4000, 44000). I am just taking
> random examples to explain the bias in the data.
>
> When I plot a histogram I just see one big bar. I feel the bins are
> not created effectively. I also tried couple of different options in
> the R hist function but with same result.
>
> hist(lane2, freq=TRUE, breaks=10);
>  hist(lane2, freq=TRUE, include.lowest=TRUE);
>

What does summary(lane2) show?  You may need to transform the data to make
it more presentable (log?).

Sean

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