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

 

 

 

 

Torsten Waldminghaus

Department of Cell Biology

Institute for Cancer Research

Rikshospitalet-Radiumhospitalet-HF

Ullernchaussen 70

0310 Oslo

tel: 47-22935973

fax: 47-22934580

e-mail: Torsten.Waldminghaus@rr-research.no

http://openwetware.org/wiki/User:Torsten_Waldminghaus

 


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