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

[James W. MacDonald]

The devel version has a different email address than the release 
version. You might try that one.

ma3mls<AT>bath<DOT>ac<DOT>uk

Best,

Jim



Daniel Brewer wrote:
> 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
>>>>
>>>
>>>
>>
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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