[Bioc-sig-seq] Assessing Transcriptome Coverage

[Abhishek Pratap]

Hi

I dont have a lot of experience with plotting large amount of data
points and clearly my question reflects that. :)

 summary(lane1)
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.      NA's
    0.000     0.040     0.180     5.186     0.620 39730.000  2264.000

Thanks for your help.

-Abhi


On Mon, Aug 17, 2009 at 3:05 PM, Sean Davis<seandavi at gmail.com> wrote:
>
>
> On Mon, Aug 17, 2009 at 3:01 PM, Abhishek Pratap <abhishek.vit at 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
>
>
>