Dear Robert,

I get the following warning in the plotSNp function:

  plotSnp(graph.par, chr.hmm)
[1] "Adding 'grey40' as a color for missing genotype.  See getPar for  
changing the defaults colors."

Warning message:
In .recycle(op$col, object) :
   The length of the vector to be recycled is less than the number of  
genotype calls

However, it seems that my object chr.hmm
has no missing genotype:
 > summary(chr.hmm@assayData$calls)
normalized-T13345-Nsp1.CEL
Min.   :1.000
1st Qu.:1.000
Median :2.000
Mean   :1.994
3rd Qu.:3.000
Max.   :3.000

Please, can you tell me about the meaning of this warning.
Best regards. Olivier

PS: Bellow the object I consider and my sessionInfo:


 > chr.hmm
HmmSnpCallSet (storageMode: lockedEnvironment)
assayData: 19865 features, 1 samples
   element names: calls, callsConfidence, predictions
experimentData: use 'experimentData(object)'
phenoData
An object of class "AnnotatedDataFrame"
   sampleNames: normalized-T13345-Nsp1.CEL
   varLabels and varMetadata description:
     gender: male/female
featureData
An object of class "AnnotatedDataFrame"
   rowNames: SNP_A-1886933, SNP_A-1902458, ..., SNP_A-4223408  (19865  
total)
   varLabels and varMetadata description:
     dbsnp_rs_id: dbsnp_rs_id
     man_fsetid: man_fsetid
     ...: ...
     fragment_length: fragment_length
     (9 total)
Annotation:  mapping250k.nsp
Hidden States:  loss ret
distance: TRUE
initialStateProbability:  0.01 0.99
chromosomeArm:
pCHOM:  0.999 0.7
callsIce:  FALSE

 > sessionInfo()
R version 2.6.0 alpha (2007-09-16 r42884)
i386-apple-darwin8.10.1

locale:
es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

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

other attached packages:
[1] VanillaICE_0.99.5        SNPchip_1.1.32            
R.utils_0.9.7            R.oo_1.4.0
[5] R.methodsS3_1.0.0        pd.mapping250k.nsp_0.3.2  
oligo_1.1.27             oligoClasses_0.99.3
[9] affxparser_1.9.5         AnnotationDbi_0.99.12     
preprocessCore_0.99.21   RSQLite_0.6-3
[13] DBI_0.2-3                Biobase_1.15.36



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