minfi::read.metharray.exp error ("The following specified files do not exist")
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@supermanrocketboy-11690
Last seen 6.1 years ago

I get an error when trying to create my RG set.

library(minfi)
baseDir <- "K:/IDATS"
targets <- read.metharray.sheet(baseDir)
RGSet <- read.metharray.exp(base = baseDir, targets = targets, verbose=T)

Error in read.metharray(files, extended = extended, verbose = verbose,  : 
  The following specified files do not exist:

 

But no files are listed. Anyone else getting this error?

I created a sample sheet (CSV) and put it in a directory containing all my IDAT files. The sample sheet contains a column called Basename, which has the full file path for each IDAT file (minus the "_Grn.idat" and "_Red.idat" suffix). 

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] minfi_1.20.0               bumphunter_1.14.0         
 [3] locfit_1.5-9.1             iterators_1.0.8           
 [5] foreach_1.4.3              Biostrings_2.42.0         
 [7] XVector_0.14.0             SummarizedExperiment_1.4.0
 [9] GenomicRanges_1.26.1       GenomeInfoDb_1.8.7        
[11] IRanges_2.8.0              S4Vectors_0.12.0          
[13] Biobase_2.32.0             BiocGenerics_0.20.0       
[15] BiocInstaller_1.24.0      

loaded via a namespace (and not attached):
 [1] mclust_5.2               base64_2.0               Rcpp_0.12.7             
 [4] lattice_0.20-33          Rsamtools_1.26.1         digest_0.6.10           
 [7] chron_2.3-47             R6_2.2.0                 plyr_1.8.4              
[10] RSQLite_1.0.0            httr_1.2.1               zlibbioc_1.20.0         
[13] GenomicFeatures_1.26.0   data.table_1.9.6         annotate_1.52.0         
[16] Matrix_1.2-7.1           preprocessCore_1.36.0    splines_3.3.1           
[19] BiocParallel_1.8.0       stringr_1.1.0            RCurl_1.95-4.8          
[22] biomaRt_2.30.0           rtracklayer_1.34.0       multtest_2.30.0         
[25] pkgmaker_0.22            openssl_0.9.4            GEOquery_2.40.0         
[28] quadprog_1.5-5           codetools_0.2-15         matrixStats_0.51.0      
[31] XML_3.98-1.4             reshape_0.8.6            GenomicAlignments_1.10.0
[34] MASS_7.3-45              bitops_1.0-6             grid_3.3.1              
[37] nlme_3.1-128             xtable_1.8-2             registry_0.3            
[40] DBI_0.5-1                magrittr_1.5             stringi_1.1.2           
[43] genefilter_1.56.0        doRNG_1.6                limma_3.30.0            
[46] nor1mix_1.2-2            RColorBrewer_1.1-2       siggenes_1.48.0         
[49] tools_3.3.1              illuminaio_0.16.0        rngtools_1.2.4          
[52] survival_2.39-5          AnnotationDbi_1.36.0     beanplot_1.2  
minfi read.metharray.exp • 3.4k views
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Entering edit mode

You will need to show the targets file that you are starting with, and probably also what is in K:/IDATS. You might also show what you get if you do

file.path(baseDir, basename(targets$Basename))

Windows can be sort of weird with network drives, especially if it's a samba mounted linux drive.

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Thru extra sleuthing, I found out that I was missing a single "_Red.idat" file for one of my samples. 

#problemsolved

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