[BioC] CRLMM warning message and null results

[Benilton Carvalho]

Hi Jenna,

can you please point me to the vignette you're looking at?

The proper way of accessing the genotype calls is:

theCalls = calls(crlmmResult)

Similarly, if you need access to the confidence scores:

theConfsProb = confs(crlmmResult) ## probability scale
theConfsIntg = confs(crlmmResult, FALSE) ## "integer" scale - uses less RAM

benilton

On 17 August 2011 16:56, Jenna Cameron <jcamer7 at uwo.ca> wrote:
> 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 at uwo.ca
> http://www.csd.uwo.ca/People/gradstudents/jcamer7/
>
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>
>
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