[BioC] CGHcall error

Vosse, S.J. S.Vosse at vumc.nl
Wed Feb 6 12:06:44 CET 2008

Dear Henrik, thanks for your suggestion to make the code more robust! We'll fix it.

Dear Daniel,

your data still has missing values (NA) in it, which causes the error. Please use the impute package or our preprocess function to impute these values, or just remove the targets with missing values (there are only 4 I think).

The error messages should be more clear, we are working on that for a future release.

Let me know if this solves your problems and feel free to contact me directly if you have any questions or suggestions.


-----Oorspronkelijk bericht-----
Van: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Namens Daniel Rico
Verzonden: Tuesday, February 05, 2008 17:21
Aan: Henrik Bengtsson
CC: bioconductor at stat.math.ethz.ch
Onderwerp: Re: [BioC] CGHcall error

hits=-2.6 tests=BAYES_00
X-USF-Spam-Flag: NO

Hi Henrik,

Sjoerd Vosse, developer of CGHcall, is having a look at my data.
Thanks to both!


Henrik Bengtsson wrote:
> On Feb 5, 2008 3:44 AM, Daniel Rico <drico at cnio.es> wrote:
>> hits=-2.6 tests=BAYES_00
>> X-USF-Spam-Flag: NO
>> Dear List,
>> I am trying to use CGHcall function from CGHcall package, trying to use
>> my own normalized and segmented dataframes (Agilent oligo Human 44A,
>> data normalized with MANOR and segmented with GLAD), buy I get this error:
>> EM algorithm started ...
>> Error en regionsdat[k, 1]:regionsdat[k, 2] : Argumento NA/NaN
>> Which I don't get when I use Wilting data from the vignette example, so
>> it could be a problem with the format of my data (although I can't find
>> any...). I wondered if maybe the dataframes were too large, but I also
>> get (another) error if I only run CGHcall with 1 chromosome:
>> EM algorithm done ...
>> Error en (posteriorfin2[profile == k, ])[, -1] :
>>   número incorreto de dimensiones # Incorrect dimension number
> Without looking at the code itself, that looks like a classical
> mistake.  When writing
>   posteriorfin2[profile == k, ]
> without an explicit 'drop=FALSE', the developer assumes that 'profile
> == k' will match
> two or more rows in the 'posteriorfin2' matrix/data.frame.  I suspect
> that in your case
> 'profile == k' is only TRUE in one case, which makes
> 'posteriorfin2[profile == k, ]'
> return a vector and not a matrix/data.frame.  This will cause the next
> subsetting '[,-1]'
> to fail, because there are no columns in a plain vector ("Incorrect
> dimension number").
> If the code would have said
>  posteriorfin2[profile == k,,drop=FALSE]
> the particular error would not show up.
> However, in the end of the day, the real question might be why you end
> up with only
> a single case for which 'profile == k' is TRUE.
> That's my $0.02
> Henrik


Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3. 
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #2256
drico at cnio.es


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