Question: Problem reading data with beadarray package
11.9 years ago by
Elizabeth McClellan • 10
Elizabeth McClellan • 10 wrote:
I am a first time user of beadarray and am having trouble simply reading in my data. I have a directory containing 12 .csv files(four columns - Illumicode, N, Mean GRN, Dev GRN), 12 .txt files (two columns - Code, Grn), and 12 .tif files from an experiment using an Illumina Human-6 v2 BeadChip. I would like to read in any or all of the arrays, but cannot seem to do so. I have tried many different functions, but everything results in an error. I am using R 2.5.1 on Windows Vista. Here is my code: > library(beadarray) Loading required package: limma Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: geneplotter Loading required package: annotate Loading required package: lattice KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: affy Loading required package: affyio Loading required package: beadarraySNP Loading required package: quantsmooth Loading required package: quantreg Loading required package: SparseM Package SparseM (0.73) loaded. To cite, see citation("SparseM") Package quantreg (4.10) loaded. To cite, see citation("quantreg") Loading required package: lodplot Loading required package: grid Attaching package: 'beadarray' The following object(s) are masked from package:limma : imageplot, plotMA > BLData<-readBeadLevelData() Error: could not find function "readBeadLevelData" > BLData<-readIllumina(textType=".txt") Found 12 arrays Error in order(dat1$ProbeID) : object "dat1" not found > BLD<-readBeadImages() Error: could not find function "readBeadImages" and R crashes every time I enter BLData<-readIllumina(textType=".csv"). I have read as many papers as I can find about the documentation for this package, as well as the R Help for package beadarray, and cannot quite figure out what "targets" or "beadtargets" should be. I have tried creating a .txt file with a list of all the .csv and .tif files I want to read in, and "readBeadTargets" accepts that, but when I try readBeadLevelData(targets) it tells me it cannot find the function "readBeadLevelData". Any help at all would be greatly appreciated, and please let me know if I need to supply anymore information. Here is my session info: R version 2.5.1 (2007-06-27) 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:  "grid" "tools" "stats" "graphics" "grDevices" "utils"  "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.4.0" "1.2.0" "1.2.0" "1.1" "4.10" "0.73" affy affyio geneplotter lattice annotate Biobase "1.14.1" "1.4.0" "1.14.0" "0.15-11" "1.14.1" "1.14.0" limma "2.10.7"
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