Unable to load any IlluminaHumanMethylation450k annotation
1
0
Entering edit mode
CPR ▴ 30
@cpr-11170
Last seen 5.2 years ago
Chicago

Dear Bioconductors,

I've been trying to set up data to run a DMR analysis for the Illumina Infinium HumanMethylation450. I have a matrix of probes and individual human id's, but I need to merge these with probe specific data, especially location data for the DMR analysis (seqLM, but still learning so open to suggestions).

I've found myself entirely unable to install any annotation file for the probes, and I've tried several.

illuminahumanmethylation450k.db ======= * Outdated, I gather.

library FDb.InfiniumMethylation.hg19  OR IlluminaHumanMethylation450kanno.ilmn12.hg19 ==== ERROR

------------------

Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Error in unloadNamespace(package) :
  namespace ‘GenomeInfoDb’ is imported by ‘GenomicRanges’ so cannot be unloaded
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,  :
  Package ‘GenomeInfoDb’ version 1.8.1 cannot be unloaded

------------------

I've tried:

remove.packages('GenomeInfoDb')
biocLite('GenomeInfoDb')

with the former providing the output:

--

Removing package from ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
(as ‘lib’ is unspecified)

--

I'm sort of at a loss. I am decent with Stats and R (but NOT a programmer), but am just figuring out how to work with and manipulate the complex datasets that are GRanges, IRanges, etc. in these deep tree lists.

I cannot for the life of me figure out why there are so many Illumina annotation files, and why none of them will load properly. Once I have that, then I can finally figure out how to subset and merge and create a dataset usable for the DMR analysis.

 

Q. How should I go about solving the above problem loading a Illumina 450K annotation data, with genomic location, gene names, and all that jazz, and then merge by probe name to my other dataset?

Many many thanks,

CPR

 

==============

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Biobase_2.32.0       IRanges_2.6.1        S4Vectors_0.10.2     BiocGenerics_0.18.0  BiocInstaller_1.22.3
 [6] repmis_0.5           ff_2.2-13            bit_1.1-12           dplyr_0.5.0          HardyWeinberg_1.5.6
[11] mice_2.25            Rcpp_0.12.6          stargazer_5.2        colorRamps_2.3       scales_0.4.0        
[16] lmtest_0.9-34        zoo_1.7-13           sjmisc_1.8           QuantPsyc_1.5        boot_1.3-18         
[21] nlme_3.1-128         MASS_7.3-45          lsr_0.5              lmSupport_2.9.4      Hmisc_3.17-4        
[26] ggplot2_2.1.0        Formula_1.2-1        survival_2.39-5      lattice_0.20-33      car_2.1-2           
[31] reshape2_1.4.1       plyr_1.8.4           doBy_4.5-15          readstata13_0.8.2    gdata_2.17.0        
[36] foreign_0.8-66       seqlm_0.1           

loaded via a namespace (and not attached):
 [1] pbkrtest_0.4-6       httr_1.2.1           RColorBrewer_1.1-2   GenomeInfoDb_1.8.3   R.cache_0.12.0      
 [6] tools_3.3.1          R6_2.1.2             rpart_4.1-10         DBI_0.4-1            lazyeval_0.2.0      
[11] mgcv_1.8-13          colorspace_1.2-6     nnet_7.3-12          raster_2.5-8         sp_1.2-3            
[16] gridExtra_2.2.1      mnormt_1.5-4         chron_2.3-47         quantreg_5.26        SparseM_1.7         
[21] sandwich_2.3-4       unmarked_0.11-0      mvtnorm_1.0-5        psych_1.6.6          AICcmodavg_2.0-4    
[26] stringr_1.0.0        digest_0.6.9         minqa_1.2.4          R.utils_2.3.0        stringdist_0.9.4.1  
[31] XVector_0.12.0       lme4_1.1-12          VGAM_1.0-2           gtools_3.5.0         acepack_1.3-3.3     
[36] R.oo_1.20.0          magrittr_1.5         modeltools_0.2-21    Matrix_1.2-6         munsell_0.4.3       
[41] R.methodsS3_1.7.1    stringi_1.1.1        multcomp_1.4-6       gvlma_1.0.0.2        zlibbioc_1.18.0     
[46] grid_3.3.1           haven_0.2.1          splines_3.3.1        GenomicRanges_1.24.2 codetools_0.2-14    
[51] latticeExtra_0.6-28  data.table_1.9.6     nloptr_1.0.4         foreach_1.4.3        MatrixModels_0.4-1  
[56] gtable_0.2.0         tidyr_0.5.1          reshape_0.8.5        assertthat_0.1       coin_1.1-2          
[61] xtable_1.8-2         tibble_1.1           iterators_1.0.8      cluster_2.0.4        TH.data_1.0-7       

 

 

FDb.InfiniumMethylation.hg19 IlluminaHumanMethylation450kanno.ilmn12.hg19 • 995 views
ADD COMMENT
0
Entering edit mode
CPR ▴ 30
@cpr-11170
Last seen 5.2 years ago
Chicago

I found what turned out to be a relatively simple solution:

I removed "Genomic Ranges" package, closed and quit R.

I then re-opened R, and ran: library("FDb.InfiniumMethylation.hg19").

It installed, but I got the error:

Error: package ‘GenomicRanges’ required by ‘GenomicFeatures’ could not be found

(no surprise), so I reinstalled it with biocLite('GenomicRanges')

I was then able to access: library("FDb.InfiniumMethylation.hg19").

It worked and I am up and running.

Hope that helps someone!

C.

ADD COMMENT

Login before adding your answer.

Traffic: 324 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6