[BioC] BUG: CGH HomHMM problem and how to debug

[Daniel Brewer]

Tried that, but unfortunately the email bounced.

Dan

James W. MacDonald wrote:
> Hi Dan,
> 
> Daniel Brewer wrote:
>> After a bit more investigation I think I have tracked down an error in
>> the runHomHMM code.
>>
>> The problem is on this line
>> rownames(segList$num.states) <- paste("Chrom", unique(input$genes$Chr))
>>
>> input$genes$Chr does not exist, only input$genes$Chrom.  Chr gets
>> created a few lines later
>> colnames(segList$genes)[colnames(segList$genes) == "Chrom"] = "Chr"
>>
>> I have used
>> update.packages(repos=biocReposList())
>>
>> to get the latest package versions,but there seems to be no new version
>> of snapCGH.  Is there an easy way to correct this within R?  How do I
>> report this apparent bug?
> 
> Send an email to the maintainer (who presumably subscribes to this list,
> but I don't know if that is true of all maintainers...).
> 
> packageDescription("snapCGH")$M
> 
> Best,
> 
> Jim
> 
> 
> 
>>
>> Thanks
>>
>> Dan
>>
>> Daniel Brewer wrote:
>>
>>> Hello,
>>>
>>> I am having a problem with the runHomHMM function of snapCGH.  I get an
>>> error which is the following:
>>>
>>>
>>>> SegInfo.Hom <- runHomHMM(test, criteria = "AIC")
>>>
>>> sample is  1   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  12  13
>>> 14  15  16  17  18  19  20  21  22
>>> sample is  2   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  12  13
>>> 14  15  16  17  18  19  20  21  22
>>> Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to
>>> array extent
>>>
>>> Does anyone know what is causing this problem or any hints on how to
>>> debug it.
>>>
>>> The test object is produced by processCGH() and looks as follows:
>>>
>>> An object of class "SegList"
>>> $M.observed
>>>               2           3
>>> [1,] -0.04886834 -0.01567368
>>> [2,] -0.03834639 -0.27615606
>>> [3,]  0.02190425 -0.12000432
>>> [4,]  0.02654545 -0.03862101
>>> [5,]  0.24526713  0.09624987
>>> 10943 more rows ...
>>>
>>> $genes
>>>       ID Row Column ProbeUID ControlType
>>> 1 1795924  56    115     5854           0
>>> 2 2862971  69     68     7165           0
>>> 3 4610962  27     92     2843           0
>>> 4 4974855  44     64     4517           0
>>> 5 2258165  45     55     4639           0
>>>
>>>
>>>  SystematicName Description Block Spot.Number Feature.Name Chr ChrStart
>>> 1       AAC67502      pSPORT     1        8695     AAC67502   1   939866
>>> 2       AI739106       pINCY     1       10676     AI739106   1   989430
>>> 3       AF016903       pINCY     1        4148     AF016903   1  1021843
>>> 4       AF148950       pINCY     1        6772     AF148950   1  1039517
>>> 5       AF296658      pSPORT     1        6919     AF296658   1  1230203
>>>   ChrEnd Position
>>> 1  941129 0.939866
>>> 2  989975 0.989430
>>> 3 1022260 1.021843
>>> 4 1041741 1.039517
>>> 5 1230592 1.230203
>>> 10943 more rows ...
>>>
>>> $design
>>> [1] -1 -1
>>>
>>>
>>> Many thanks
>>>
>>> Daniel
>>>
>>
>>
> 
> 

-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109
Fax: +44 (0) 20 8722 4141

Email: daniel.brewer at icr.ac.uk

**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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