Dear Elizabeth,

It might be worth updating your version of beadarray to the current release version (1.6.0 - you'll need to install R-2.6.0).  The function readBeadLevelData() is no longer used in the package, so this is cause of some of your error messages.

It also looks as if your data is in a slightly different format to what we usually see.  The files which contain the bead level data (.txt files in your case) usually have Code, Grn, GrnX and GrnY columns as a minimum.  Perhaps you can send me a few example .txt files (zipped up and off-list) so that I can take a closer look?

The targets information is a data.frame which contains information about each array (array names, sample info, etc).  For Human 6 v2 BeadChips, your targets information will have 12 rows per BeadChip (since there are 6 arrays and 2 strips per array) and as many columns as you wish.  I find is useful to have a column containing the arrayNames.  See below for a simple example from a Mouse 6 v1 BeadChip.

> targets
       arrayNames sampleNames
1  1377192001_A_1       test1
2  1377192001_A_2       test1
3  1377192001_B_1       test2
4  1377192001_B_2       test2
5  1377192001_C_1       test3
6  1377192001_C_2       test3
7  1377192001_D_1       test4
8  1377192001_D_2       test4
9  1377192001_E_1       test5
10 1377192001_E_2       test5
11 1377192001_F_1       test6
12 1377192001_F_2       test6
> bldata = readIllumina(arrayNames=targets$arrayNames, useImages=FALSE, textType=".txt", targets=targets)

I hope this helps.  Best wishes,

Matt

**************
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" 



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