[BioC] CGH HomHMM problem and how to debug

[Daniel Brewer]

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
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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