Question: minfi v1.14 through champ: read.450k error with file path name
0
gravatar for jeroen
3.9 years ago by
jeroen0
Belgium
jeroen0 wrote:

Hi,

Since I did an R update including updating the minfi package to v1.14 (which I now deeply regret), an error keeps preventing me from reading my .idat files. I'm using the load.champ function which entails read.450k of the minfi package. The file path he's trying to read is wrong and reads like "c:/myDir/c:/myDir/..."

Probably, it's a simple bug which was also mentioned and fixed here. I didn't have it in minfi v1.12 so it probably has returned.

Thanks in advance for any help,

Jeroen

setwd("C:/myDir")
library("ChAMP", lib.loc="~/R/win-library/3.1")
myLoad = champ.load(directory = "C:/myDir", methValue = "B")
[1] "C:/myDir/Samplesheet_BS_ResistantvsNonresistant_AllLines.csv"
Error in read.450k(files, extended = extended, verbose = verbose) : 
  The following specified files do not exist:C:/myDir/C:/myDir/3999876054/3999876054_R01C02_Grn.idat, C:/myDir/C:/myDir/3999876054/3999876054_R02C02_Grn.idat, C:/myDir/C:/myDir/3999876054/3999876054_R03C02_Grn.idat, C:/myDir/C:/myDir/3999876054/3999876054_R04C02_Grn.idat, C:/myDir/C:/myDir/3999876054/3999876054_R05C02_Grn.idat, C:/myDir/C:/myDir/3999876054/3999876054_R06C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R01C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R02C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R03C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R04C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R05C02_Grn.idat, C:/myDir/C:/myDir/3998568147/3998568147_R06C02_Grn.idat

---------------------- Session Info ----------------------

R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252    LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C                  
[5] LC_TIME=Dutch_Belgium.1252    

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

other attached packages:
 [1] ChAMP_1.4.1                       Illumina450ProbeVariants.db_1.4.0 ChAMPdata_1.6.0                   minfi_1.14.0                     
 [5] bumphunter_1.8.0                  locfit_1.5-9.1                    iterators_1.0.7                   foreach_1.4.2                    
 [9] Biostrings_2.36.4                 XVector_0.8.0                     GenomicRanges_1.20.5              GenomeInfoDb_1.4.2               
[13] IRanges_2.2.7                     S4Vectors_0.6.3                   lattice_0.20-33                   Biobase_2.28.0                   
[17] BiocGenerics_0.14.0              
minfi champ illumina 450k • 830 views
ADD COMMENTlink written 3.9 years ago by jeroen0
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