[BioC] CRLMM warning message and null results
beniltoncarvalho at gmail.com
Wed Aug 17 18:57:36 CEST 2011
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
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)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=en_US.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  genomewidesnp6Crlmm_1.0.4 hapmapsnp6_1.3.3
>  crlmm_1.8.11 oligo_1.14.0
>  oligoClasses_1.12.2 Biobase_2.10.0
> loaded via a namespace (and not attached):
>  affxparser_1.22.1 affyio_1.18.0
>  annotate_1.28.1 AnnotationDbi_1.12.1
>  Biostrings_2.18.4 bit_1.1-7
>  DBI_0.2-5 ellipse_0.3-5
>  ff_2.2-3 genefilter_1.32.0
>  IRanges_1.8.9 mvtnorm_0.9-95
>  preprocessCore_1.12.0 RSQLite_0.9-4
>  splines_2.12.1 survival_2.36-2
>  tcltk_2.12.1 tools_2.12.1
>  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.
> Jenna Butler
> Jenna L Butler
> PhD Computer Science Candidate 2014
> University of Western Ontario, Canada
> jcamer7 at uwo.ca
> [[alternative HTML version deleted]]
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)
More information about the Bioconductor