Question: minfi package QC report error?
0
gravatar for Brian Smith
5.0 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Hi,

I was trying to use the minfi package to process my methylation data. I get an error when I try to generate the QC report.  I get the methylation values ok, so my problem appears to be just in generating the report. Here is my code so far:

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

> library(minfi)
>   library(IlluminaHumanMethylation450kmanifest)
>   
>   RGset <- read.450k.exp(base = tidir, targets = annfile3)
>   
>   MSet.raw <- preprocessRaw(RGset)
>   pd <- pData(RGset)
>   meth <- getMeth(MSet.raw)
>   unmeth <- getUnmeth(MSet.raw)
>   beta <- getBeta(MSet.raw)
>   mval <- getM(MSet.raw)

> beta[1:3,1:3]

           9880171164_R01C01 9880171164_R02C01 9880171164_R03C01
cg00050873         0.6787634         0.5947426         0.5972073
cg00212031         0.5895652         0.3651685         0.6581818
cg00213748         0.6075949         0.4461911         0.5461422


>   qcReport(RGset, sampNames = pd$Sample_Name, sampGroups = pd$Sample_Group, pdf = paste(odir,"qc/qcReport.pdf",sep=''))
Error in densityBeanPlot(rgSet[, sampleIdx], sampGroups = sampGroups[sampleIdx],  : 
  lazy-load database 'P' is corrupt
In addition: Warning messages:
1: In densityBeanPlot(rgSet[, sampleIdx], sampGroups = sampGroups[sampleIdx],  :
  restarting interrupted promise evaluation
2: In densityBeanPlot(rgSet[, sampleIdx], sampGroups = sampGroups[sampleIdx],  :
  internal error -3 in R_decompress1

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

My data is for 2 chips (i.e. 24 samples).

My session info is:

 

 

 


> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (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  splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] methylumi_2.8.0                            matrixStats_0.10.3                         ggplot2_1.0.0                             
 [4] reshape2_1.4                               scales_0.2.4                               IlluminaHumanMethylation450kmanifest_0.4.0
 [7] BiocInstaller_1.12.1                       minfi_1.8.9                                bumphunter_1.2.0                          
[10] iterators_1.0.7                            Biostrings_2.30.1                          GenomicRanges_1.14.4                      
[13] XVector_0.2.0                              IRanges_1.20.7                             Biobase_2.22.0                            
[16] BiocGenerics_0.8.0                         lsr_0.3.2                                  compute.es_0.2-4                          
[19] sm_2.2-5.4                                 imputation_2.0.1                           locfit_1.5-9.1                            
[22] TimeProjection_0.2.0                       Matrix_1.1-4                               timeDate_3010.98                          
[25] lubridate_1.3.3                            gbm_2.1                                    lattice_0.20-29                           
[28] survival_2.37-7                            RobustRankAggreg_1.1                       impute_1.36.0                             
[31] reshape_0.8.5                              zoo_1.7-11                                 data.table_1.9.2                          
[34] foreach_1.4.2                              foreign_0.8-61                             languageR_1.4                             
[37] preprocessCore_1.24.0                      gtools_3.4.1                              

loaded via a namespace (and not attached):
 [1] annotate_1.40.1      AnnotationDbi_1.24.0 base64_1.1           beanplot_1.2         codetools_0.2-9      colorspace_1.2-4     DBI_0.3.1           
 [8] digest_0.6.4         doRNG_1.6            genefilter_1.44.0    grid_3.0.1           gtable_0.1.2         illuminaio_0.4.0     itertools_0.1-3     
[15] limma_3.18.13        MASS_7.3-35          mclust_4.4           memoise_0.2.1        multtest_2.18.0      munsell_0.4.2        nlme_3.1-118        
[22] nor1mix_1.2-0        pkgmaker_0.22        plyr_1.8.1           proto_0.3-10         R.methodsS3_1.6.1    RColorBrewer_1.0-5   Rcpp_0.11.3         
[29] registry_0.2         rngtools_1.2.4       RSQLite_0.11.4       siggenes_1.36.0      stats4_3.0.1         stringr_0.6.2        tools_3.0.1         
[36] XML_3.95-0.2         xtable_1.7-4    

minfi illumina methylation • 957 views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Brian Smith120
1

Maybe try a fresh session (started with R --vanilla). You could also try reinstalling minfi.

ADD REPLYlink written 5.0 years ago by Dan Tenenbaum8.2k
Answer: minfi package QC report error?
0
gravatar for Brian Smith
5.0 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Whoa! That worked (restarting R)!

If in doubt, restart :)) 

ADD COMMENTlink written 5.0 years ago by Brian Smith120
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