[BioC] chipAlongChrom problem in Ringo
toedling at ebi.ac.uk
Tue Jan 27 14:47:17 CET 2009
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.
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!
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