[BioC] error on loading ratioConvert() in minfi

[Jia, Li (NIH/NCI) [C]]

Hi Kasper,

You are right, I restarted the new session, it works. But when I tried to move along the analysis to generate the GenomeratioSet, it has another error message:

> gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
  solving row 1: range cannot be determined from the supplied arguments (too many NAs)

Could you please let me know what's wrong with this?

Thanks a lot,
Li


From: Kasper Daniel Hansen <khansen at jhsph.edu<mailto:khansen at jhsph.edu>>
Date: Thu, 22 May 2014 22:23:48 -0400
To: "Jia, Li (NIH/NCI) [C]" <li.jia2 at nih.gov<mailto:li.jia2 at nih.gov>>
Cc: "guest [guest]" <guest at bioconductor.org<mailto:guest at bioconductor.org>>, "bioconductor at r-project.org<mailto:bioconductor at r-project.org>" <bioconductor at r-project.org<mailto:bioconductor at r-project.org>>
Subject: Re: [BioC] error on loading ratioConvert() in minfi


On Wed, May 21, 2014 at 1:59 PM, Jia, Li (NIH/NCI) [C] <li.jia2 at nih.gov<mailto:li.jia2 at nih.gov>> wrote:
library(minfi)
> ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), keepCN = TRUE)

Well, it works fine for me.  Perhaps look at sessionInfo() after error and verify you're on a new minfi version.

> library(minfiData)
> ratioSet <- ratioConvert(MsetEx, what = c("beta", "M", "both"), keepCN = TRUE)
> sessionInfo()
R version 3.1.0 Patched (2014-04-26 r65503)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8

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

other attached packages:
 [1] minfiData_0.6.0
 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [3] IlluminaHumanMethylation450kmanifest_0.4.0
 [4] minfi_1.10.1
 [5] bumphunter_1.4.0
 [6] locfit_1.5-9.1
 [7] iterators_1.0.7
 [8] foreach_1.4.2
 [9] Biostrings_2.32.0
[10] XVector_0.4.0
[11] GenomicRanges_1.16.3
[12] GenomeInfoDb_1.0.2
[13] IRanges_1.22.6
[14] lattice_0.20-29
[15] Biobase_2.24.0
[16] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] annotate_1.42.0       AnnotationDbi_1.26.0  base64_1.1
 [4] beanplot_1.1          codetools_0.2-8       DBI_0.2-7
 [7] digest_0.6.4          doRNG_1.6             genefilter_1.46.0
[10] grid_3.1.0            illuminaio_0.6.0      limma_3.20.1
[13] MASS_7.3-31           matrixStats_0.8.14    mclust_4.3
[16] multtest_2.20.0       nlme_3.1-117          nor1mix_1.1-4
[19] pkgmaker_0.20         plyr_1.8.1            preprocessCore_1.26.0
[22] R.methodsS3_1.6.1     RColorBrewer_1.0-5    Rcpp_0.11.1
[25] registry_0.2          reshape_0.8.5         rngtools_1.2.4
[28] RSQLite_0.11.4        siggenes_1.38.0       splines_3.1.0
[31] stats4_3.1.0          stringr_0.6.2         survival_2.37-7
[34] tools_3.1.0           XML_3.98-1.1          xtable_1.7-3
[37] zlibbioc_1.10.0