Hello everyone,

I am attempting to run the sample commands given in the CRLMM version 2 vignette. After loading the crlmm library and hapmapsnp6 library I have run the following commands:



Jenna's R> path <- system.file("celFiles", package="hapmapsnp6")
Jenna's R> celFiles <- list.celfiles(path, full.names=TRUE)
Jenna's R> system.time(crlmmResult <- crlmm(celFiles, verbose=TRUE))
Loading required package: genomewidesnp6Crlmm
Welcome togenomewidesnp6Crlmmversion 1.0.4
Loading annotations and mixture model parameters.
Processing 3 files.
  |==================================================| 100%
Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Calling 906600 SNPs... Done.
   user  system elapsed 
281.242   7.256 298.400 
Warning message:
In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]],  :
  Recalibration not possible. Possible cause: small sample size.



After I get this when I attempt to look at the results, using crlmmResult[["calls"]][1:10, ] I get NULL. There are no results anywhere in crlmmResults.  I have tried running this with both hapmapsnp5 and hapmapsnp6.


Here is my session information:
Jenna's R> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i686-pc-linux-gnu (32-bit)


locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       


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


other attached packages:
[1] genomewidesnp6Crlmm_1.0.4 hapmapsnp6_1.3.3         
[3] crlmm_1.8.11              oligo_1.14.0             
[5] oligoClasses_1.12.2       Biobase_2.10.0           


loaded via a namespace (and not attached):
 [1] affxparser_1.22.1     affyio_1.18.0        
 [3] annotate_1.28.1       AnnotationDbi_1.12.1 
 [5] Biostrings_2.18.4     bit_1.1-7            
 [7] DBI_0.2-5             ellipse_0.3-5        
 [9] ff_2.2-3              genefilter_1.32.0    
[11] IRanges_1.8.9         mvtnorm_0.9-95       
[13] preprocessCore_1.12.0 RSQLite_0.9-4        
[15] splines_2.12.1        survival_2.36-2      
[17] tcltk_2.12.1          tools_2.12.1         
[19] xtable_1.5-6         




If anyone has come across this or can provide me with some guidance I would greatly appreciate it. Thank you in advance.


Sincerely, 
Jenna Butler
--
Jenna L Butler
PhD Computer Science Candidate 2014
University of Western Ontario, Canada
jcamer7@uwo.ca    
http://www.csd.uwo.ca/People/gradstudents/jcamer7/

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