[BioC] error in runBioHMM() (package snapCGH)

[Wolfgang Raffelsberger]

Dear list,

when analyzing Agilent 44k (human) CGH data* *using the function 
runBioHMM() from the library snapCGH I've run into an error message 
described below. 
Curiously this error has never occurred before although I've been using 
more or less the same code with previous data-sets where the code was 
working well ! So I wonder if there's something special with may data, 
but I can't find any particular anomalies in the data$M.observed (eg 
I've checked that there are no NAs ...)
A summary of the data didn't indicate anything "completely" different to 
the other arrays, at least nothing that gave the impression beyond those 
differences due to the nature/biology of the biospies.
If you would like to get a copy of the real data, pls let me know, of 
course the file-size would be way to large for attaching to this message.

As the function runBioHMM() doesn't contain a line containing "if 
((phi[3, t - 1] + max(-1e+05, log(BFGS.trans.mat[ ..." I'm stuck to get 
some clues of what may have caused the problem.
Note that other segmentation functions form the same package like 
runDNAcopy() or runGALD() did work without problems !!

I'm running code like :

library(limma); library(snapCGH); library(DNAcopy); library(GLAD); 
library(smoothseg)
RG1 <- read.maimages(file=mySamples,columns=extrCols1,other.columns= 
extrOtherCols,source = "agilent")
 MA1 <- normalizeBetweenArrays(RG1,method="Aquantile")
 MA1$design <- rep(-1,ncol(MA1$M))
 MA1_snpCGH <- processCGH(MA1, maxChromThreshold = 
length(na.omit(unique(MA1$genes$Chr))) )
 MA1_snpCGH$genes$Position <- round(MA1_snpCGH$genes$Position,6)        
# transform to Mb scale
 ## checking (some of) my data
  summary( MAagil_snpCGH$M.observed[,155:156] )    ## gives :
    M.111_CN_18     M.111_CN_19
    Min.   :-4.856865      Min.   :-2.919297    
    1st Qu.:-0.243359      1st Qu.:-0.235424    
    Median :-0.044505      Median :-0.039601    
    Mean   : 0.007306      Mean   : 0.001244    
    3rd Qu.: 0.163834      3rd Qu.: 0.152406    
    Max.   : 7.773869      Max.   : 4.161682 

 MA1_snpCGH$M <- MA1_snpCGH$M.observed
## and here I (consitently) get the error : (message truncated to show 
the end)
sample is  153   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  12  13  
14  15  16  17  18  19  20  21  22  23  24
sample is  154   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  12  13  
14  15  16  17  18  19  20  21  22  23  24
sample is  155   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  12  13  
14  15  16  17  18  19  20  21  22  23  24
sample is  156   Chromosomes: 1  2  3  4  5  6  7  8  9  10  11  Error 
in if ((phi[3, t - 1] + max(-1e+05, log(BFGS.trans.mat[[t - 1]][3,  :
  missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the 
first 50)
Error in res$nstates.list : $ operator is invalid for atomic vectors


## for completeness:

 > sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
 [1] splines   grid      tools     stats     graphics  grDevices utils   
 [8] datasets  methods   base    

other attached packages:
 [1] smoothseg_0.0.1     OCplus_1.16.0       akima_0.5-1       
 [4] snapCGH_1.10.0      aCGH_1.16.0         sma_0.5.15        
 [7] multtest_1.22.0     cluster_1.11.11     GLAD_1.18.0       
[10] DNAcopy_1.16.0      tilingArray_1.20.0  pixmap_0.4-9      
[13] geneplotter_1.20.0  annotate_1.20.1     xtable_1.5-4      
[16] AnnotationDbi_1.4.1 genefilter_1.22.0   survival_2.34-1   
[19] vsn_3.8.0           lattice_0.17-15     strucchange_1.3-4 
[22] sandwich_2.1-0      zoo_1.5-4           RColorBrewer_1.0-2
[25] affy_1.20.0         Biobase_2.2.1       limma_2.16.3      

loaded via a namespace (and not attached):
[1] DBI_0.2-4            KernSmooth_2.22-22   RSQLite_0.7-1      
[4] affyio_1.10.1        preprocessCore_1.4.0



Any suggestions how to resolve this problem would be very much appreciated !
Wolfgang Raffelsberger

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC,  
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr