Hi,
On Tue, Sep 16, 2008 at 5:50 AM, cruckert <[EMAIL PROTECTED]> wrote:
>
> I've gone through the steps in the online vignette (Total Copy Number
> Analysis (5.0 & 6.0)), but everytime I run process(ce) I got the
> following error message:
>
> Exception: Something is wrong with the data. Too many non-finite
> values: 5385 (56.8% > 20.0%)
> at throw(Exception(...))
> at throw.default(sprintf("Something is wrong with the data. Too many
> non-finit
> at throw(sprintf("Something is wrong with the data. Too many non-
> finite values
> at getRawCnData.CopyNumberChromosomalModel(this, ceList = ceList,
> refList = rf
> at getRawCnData(this, ceList = ceList, refList = rfList, chromosome
> = chr, ...
> at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> verbose = v
> at fit(this, ..., .retResults = FALSE, verbose = verbose)
> at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> = "png", p
> at plot(model, path = path, imageFormat = "png", plotband =
> plotband, arrays =
> at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
> = chromos
> at writeGraphs(this, arrays = arrays, chromosomes =
> chromosomes, ..., verbose
> at process.ChromosomeExplorer(ceglad)
> at process(cegl
it is probably because of noisy data on ChrX and ChrY. Non-finite
values can be introduced because non-positive estimates along the way
get log transformed. A long time ago I added that as a sanity check
for this and I selected 20% as an ad hoc threshold to catch my/our
attention.
But first, what is your sessionInfo()? Do you follow the vignette
exactly or do you change something, that is very important to know.
Could you also tell us more about your data, e.g. what chip type and
how many arrays do you have? How many females and males?
>
> Is there any parameter in the previous steps I can change to avoid
> this error. I have already tried:
> ce = ChromosomeExplorer(cbs, maxNAFraction=9/10)
> without success.
Where did you find out about that? (If there is an URL saying so it
needs to be corrected). It's true that there is the option
'maxNAFraction', but you should pass it to process() not to the
constructor.
Cheers
/Henrik
>
> >
>
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