[aroma.affymetrix] Re: SNP6 CNV analysis with Technical replicates

2009-06-10 Thread marco
works fine! thanks for the help .. On 9 Juni, 21:19, Henrik Bengtsson wrote: > I see, the first argument to CbsModel() has to be a set, not a file, > so try to wrap 'ceR1' up in one.  The easiest way to get a set of the > correct class with the correct parameter settings, do: > > cesR1 <- newIn

[aroma.affymetrix] Re: SNP6 CNV analysis with Technical replicates

2009-06-09 Thread Henrik Bengtsson
I see, the first argument to CbsModel() has to be a set, not a file, so try to wrap 'ceR1' up in one. The easiest way to get a set of the correct class with the correct parameter settings, do: cesR1 <- newInstance(ces1, files=list(ceR1)); cbs <- CbsModel(ceR1, ceR2); Does this work? /H On Tue

[aroma.affymetrix] Re: SNP6 CNV analysis with Technical replicates

2009-06-09 Thread marco
Henrik seems like it does not work. I went on to R2.9.0 with latest version of aroma but I get the following: I tried also the getAverageFile() function but with the same result. I guess the two functions do the same thing or a very similar one? Marco cdf <- AffymetrixCdfFile$byChipType(

[aroma.affymetrix] Re: SNP6 CNV analysis with Technical replicates

2009-06-08 Thread Henrik Bengtsson
Hi. On Mon, Jun 8, 2009 at 1:53 PM, marco wrote: > > Dear Henrik, > >  I have 2 samples hzbridiyed on SNP6 in respctively 5 and 6 > replicates. I would like to pool them ann estimate the relative CNVs. > Is this fragment of code doing that? Or you have any other > suggestions? > > > cdf      <- A