Question: problems reading Illumina files using BeadExplorer
gravatar for Vitalina Komashko
12.7 years ago by
Vitalina Komashko10 wrote:
Dear all, I am trying to use BeadExplorer to load Illumina Mouse8 arrays for analysis. I used the latest BeadStudio software version to generate expression data, but it actually does not give summary files such as gene.profile.csv and qcinfo.csv, so I had to save them separately when I opened the data. Here the error I constantly get when I load the data: > data<-beadAnalysis() Read C:/Program Files/R/R-2.4.0/data/mouse_copy_sample_gene_profile.csv Normalised data... Generated qc data... Error in sum(detExprs(beadData)[, i] > value) : subscript out of bounds In addition: Warning message: no non-missing arguments to min; returning Inf There are no header lines when I save my data directly from BeadStudio. Does it matter? R info: > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "tcltk" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: convert marray limma BeadExplorer tkWidgets DynDoc "1.8.0" "1.12.0" "2.9.1" "1.2.0" "1.12.0" "1.12.0" R2HTML affy affyio widgetTools Biobase "1.58" "1.12.0" "1.2.0" "1.10.0" "1.12.1" I will appreciate any help. Thank you! Vitalina.
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