Bug?: crlmm and cdfName not valid
1
0
Entering edit mode
mcgaugheyd • 0
@mcgaugheyd-11610
Last seen 19 months ago

Having an issue with genotype.Illumina with crlmm

​test <- genotype.Illumina(
                  sampleSheet=sampleSheet,
                  cdfName = 'humanomniexpexome8v1p1b')

I get this error:

Instantiate CNSet container.
Initializing container for genotyping and copy number estimation
Loading required package: humanomniexpexome8v1p1bCrlmm
If humanomniexpexome8v1p1bCrlmm is installed on an alternative location, please load it manually by using library(humanomniexpexome8v1p1bCrlmm,lib.loc='/Altern/Lib/Loc')
Error in getFeatureData(cdfName, copynumber = TRUE, genome = genome) : 
  Package humanomniexpexome8v1p1bCrlmm could not be found.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘humanomniexpexome8v1p1bCrlmm’

> traceback()
4: stop("Package ", pkgname, " could not be found.")
3: getFeatureData(cdfName, copynumber = TRUE, genome = genome)
2: constructInf(sampleSheet = sampleSheet, arrayNames = arrayNames, 
       path = path, arrayInfoColNames = arrayInfoColNames, highDensity = highDensity, 
       sep = sep, fileExt = fileExt, XY = XY, cdfName = cdfName, 
       verbose = verbose, batch = batch, saveDate = saveDate)
1: genotype.Illumina(sampleSheet = sampleSheet, path = "/Volumes/ThunderBay/PROJECTS/test", 
       call.method = "crlmm", cdfName = "humanomniexpexome8v1p1b")

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bit64_0.9-5           dplyr_0.5.0           purrr_0.2.2           readr_1.0.0           tidyr_0.6.0           tibble_1.2            ggplot2_2.1.0         tidyverse_1.0.0      
 [9] data.table_1.9.6      crlmm_1.30.0          preprocessCore_1.34.0 oligoClasses_1.34.0   BiocInstaller_1.22.3  ff_2.2-13             bit_1.1-12           

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                plyr_1.8.4                 GenomeInfoDb_1.8.7         XVector_0.12.1             iterators_1.0.8            tools_3.3.1               
 [7] zlibbioc_1.18.0            base64_2.0                 gtable_0.2.0               RSQLite_1.0.0              lattice_0.20-34            Matrix_1.2-7.1            
[13] foreach_1.4.3              DBI_0.5-1                  parallel_3.3.1             mvtnorm_1.0-5              Biostrings_2.40.2          S4Vectors_0.10.3          
[19] IRanges_2.6.1              stats4_3.3.1               grid_3.3.1                 Biobase_2.32.0             ellipse_0.3-8              R6_2.2.0                  
[25] VGAM_1.0-2                 magrittr_1.5               scales_0.4.0               codetools_0.2-15           matrixStats_0.50.2         BiocGenerics_0.18.0       
[31] GenomicRanges_1.24.3       splines_3.3.1              assertthat_0.1             rsconnect_0.4.3            SummarizedExperiment_1.2.3 colorspace_1.2-6          
[37] lazyeval_0.2.0             munsell_0.4.3              openssl_0.9.4              chron_2.3-47               RcppEigen_0.3.2.9.0        illuminaio_0.14.0         
[43] affyio_1.42.0             
software error crlmm • 654 views
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0
Entering edit mode
Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 5 months ago
Australia

This error message means that the chip-specific package you need hasn't been installed.

However, installing it in the usual way with biocLite() is currently impossible, because I haven't added it to Bioconductor!

Try downloading from http://bioinf.wehi.edu.au/folders/mritchie/humanomniexpexome8v1p1bCrlmm_1.0.1.tar.gz

and installing with the command

R CMD INSTALL humanomniexpexome8v1p1bCrlmm_1.0.1.tar.gz

Hopefully this will get you going again.

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