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

[James W. MacDonald]

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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.