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

[Daniel Brewer]

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?

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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