[BioC] chipAlongChrom problem in Ringo

[Jianping Jin]

Hi Joern,

I used the code on the PLos article to summarize the GO terms with the 
ChIP-enriched regions. But I got some problems in sigGOTable:

NFRes <- sigGOTable(NFOnlygenes)
.
.
         Level 2:       18 nodes to be scored   (17 eliminated genes)

         Level 1:       1 nodes to be scored    (17 eliminated genes)
Error in .local(object, ...) :
  Use: topGOdata, topGOresult_1, topGOresult_2, ..., "parameters".

What is the problem and can we fix it?

thanks,

Jianping


--On Tuesday, January 27, 2009 10:52 AM -0500 Jianping Jin 
<jjin at email.unc.edu> wrote:

> 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?
>
> thanks,
>
> Jianping
>
> --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



##################################
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