[BioC] chipAlongChrom problem in Ringo

Jianping Jin jjin at email.unc.edu
Tue Jan 27 16:52:40 CET 2009

Hi Joern,

You are right. I need to generate y0 for the plot.

Here is another trouble:

> plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeAnno, 
gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6))
Error in as.double(x) :
  cannot coerce type 'S4' to vector of type 'double'

chipAlongChrom works with expression data while plot works with x and y 
coordinates. How chersX can be plotted with smoothX?



--On Tuesday, January 27, 2009 1:47 PM +0000 Joern Toedling 
<toedling at ebi.ac.uk> wrote:

> 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

Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu

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