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Elizabeth McClellan
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10
@elizabeth-mcclellan-2442
Last seen 10.3 years ago
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:
[1] "grid" "tools" "stats" "graphics" "grDevices"
"utils"
[7] "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"