[BioC] error on loading ratioConvert() in minfi

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

Hi Kasper,

We just upgraded to version 1.10.0, but it still doesn't work.

> library(minfi)
> ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), keepCN = TRUE)
Error: could not find function "ratioConvert"

Thanks,
Li

From: Kasper Daniel Hansen <khansen at jhsph.edu<mailto:khansen at jhsph.edu>>
Date: Wed, 21 May 2014 13:33:54 -0400
To: "guest [guest]" <guest at bioconductor.org<mailto:guest at bioconductor.org>>
Cc: "bioconductor at r-project.org<mailto:bioconductor at r-project.org>" <bioconductor at r-project.org<mailto:bioconductor at r-project.org>>, "Jia, Li (NIH/NCI) [C]" <jial2 at mail.nih.gov<mailto:jial2 at mail.nih.gov>>
Subject: Re: [BioC] error on loading ratioConvert() in minfi

Upgrade, minfi 1.6.0 is ancient.

Kasper


On Wed, May 21, 2014 at 11:45 AM, guest [guest] <guest at bioconductor.org<mailto:guest at bioconductor.org>> wrote:
Dear Users,

I tried to convert the set to ratioset using ratioConvert(), but it has an error message

> ratioConvert(RGset, what = c("beta", "M", "both"), keepCN = TRUE)
Error: could not find function "ratioConvert"

I installed minfi and load the library, I don't get it why this error message coming out?

Thanks,


 -- output of sessionInfo():

> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-unknown-linux-gnu (64-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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] FDb.UCSC.snp137common.hg19_1.0.0
 [2] GenomicFeatures_1.12.4
 [3] IlluminaHumanMethylation450k.db_2.0.7
 [4] org.Hs.eg.db_2.9.0
 [5] RSQLite_0.11.4
 [6] DBI_0.2-7
 [7] AnnotationDbi_1.22.6
 [8] minfiData_0.3.4
 [9] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3
[10] IlluminaHumanMethylation450kmanifest_0.4.0
[11] methylumi_2.6.1
[12] ggplot2_0.9.3.1
[13] reshape2_1.4
[14] scales_0.2.4
[15] lumi_2.12.0
[16] minfi_1.6.0
[17] Biostrings_2.28.0
[18] GenomicRanges_1.12.5
[19] IRanges_1.18.4
[20] reshape_0.8.5
[21] lattice_0.20-29
[22] Biobase_2.22.0
[23] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         annotate_1.38.0
 [4] beanplot_1.1          BiocInstaller_1.10.4  biomaRt_2.16.0
 [7] bitops_1.0-6          BSgenome_1.28.0       colorspace_1.2-4
[10] digest_0.6.4          grid_3.0.3            gtable_0.1.2
[13] illuminaio_0.2.0      KernSmooth_2.23-12    limma_3.16.8
[16] MASS_7.3-33           Matrix_1.1-3          matrixStats_0.8.14
[19] mclust_4.3            mgcv_1.7-29           multtest_2.16.0
[22] munsell_0.4.2         nleqslv_2.1.1         nlme_3.1-117
[25] nor1mix_1.1-4         plyr_1.8.1            preprocessCore_1.22.0
[28] proto_0.3-10          R.methodsS3_1.6.1     RColorBrewer_1.0-5
[31] Rcpp_0.11.1           RCurl_1.95-4.1        Rsamtools_1.12.4
[34] rtracklayer_1.20.4    siggenes_1.34.0       splines_3.0.3
[37] stats4_3.0.3          stringr_0.6.2         survival_2.37-7
[40] tools_3.0.3           XML_3.98-1.1          xtable_1.7-3
[43] zlibbioc_1.6.0


--
Sent via the guest posting facility at bioconductor.org<http://bioconductor.org>.

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