[BioC] chipAlongChrom problem in Ringo

[Joern Toedling]

Hi Jianping,

I presume you created the histogram as we specified in the PLoS CB
tutorial article. The error message literally means that the object "y0"
does not exist, and you need to create it before drawing the histogram.
One option for creating  y0, which is the variable holding the threshold
for calling ChIP-enriched region, is also given in the tutorial as
 y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99)
Hope this helps.

Joern

Jianping Jin wrote:
> Thanks Joern.
>
> I re-ran Exonerate and it worked out for me.
>
> There is anther question. When I tried to find ChIP-enriched regions
> between two experiment conditions with histogram (smoothed reporter
> level[log2] versus Percent of Total) by print(h), the error messages
> on histograms of both conditions appear:
>
> Error using packet 1 (or 2) object "y0" not found.
>
> Both histograms look like normal distribution and very similar, though
> condition one shifts a bit left around zero. This may be caused by the
> fact that there is no mixture of two underlying distribution was
> found. I wanted to make sure if the "no object y(0) being found itself
> is the source of the error (so I may want to try other normalization
> method) or something else I missed.
>
> Please take a look at the attached file. Appreciate your help!
>
> Jianping
>

-- 
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk