[BioC] Missing Autocorrelation in Ringo

[Joern Toedling]

Hello,

to clarify, do you mean that the plot does not show anything or that the plot
indicates that there is no correlation? Is there an error message or warning?
If so, what does it say?

Further questions that could help me to figure out what is going on.
What is the result of
str(exAc)
ls(annoObject)
head(annoObject["1.start"])

Note that if your Agilent ChIP-chip files follow their convention to encode
the probe position in a colum called "SystematicName" then you can also use
the function "extractProbeAnno" on the RGList to obtain a probeAnno object.

Last but not least, what is the output of sessionInfo()? Please always specify
that when posting a question on the Bioconductor mailing list so that we can
figure out if there might be problem with the package versions.

Best regards,
Joern0


On Mon, 29 Jun 2009 14:17:00 +0200, Torsten Waldminghaus wrote
> Dear all,
> 
> I started using the Ringo package to analyze ChIP on Chip data and tried
> to make a nice plot of my nice autocorrelation. However, the plot shows
> no autocorrelation of neighbouring probes. This is unlikely to be
> because of the bad data, because I see really nice peaks when I plot
> signals on the chromosomal position and it fits very well with published
> data. If anybody has a suggestion what could be wrong or how I could
> find out what's wrong I would be happy.
> 
> This is what I do in more detail:
> 
> > RG <- read.maimages(files,"agilent")#read in array data
> 
> I wrote an annotation file which looks like this ("POSITIONS" and
> "PROBE_ID" come from the RG file above):
> 
> > annotationFile[1:3,]
> 
>   CHROMOSOME PROBE_ID POSITION LENGTH
> 
> 1          1        2   218268     60
> 
> 2          1        3  2239049     60
> 
> 3          1        6  3448934     60
> 
> This I used to make a probeAnno object like this:
> 
> > annoObject<-posToProbeAnno (annotationFile)
> 
> Than I calculate autocorrelation:
> 
> > exAc<-autocor(RG,probeAnno=annoObject, chrom="1",lag.max=1000)
> 
> And plot:
> 
> > plot(exAc)
> 
> Thanks for any help,
> 
> Torsten