[BioC] beadarray: combining several beadsummary data objects

[Asta Laiho]

I am using beadarray to read in raw data from two Illumina mouse 6 bead chips. 
I am trying to read in  4 arrays (two arrays per sample) per chip. However, there 
is a problem I didn't manage to solve when I try to combine the data sets from two 
different  chips. 

Combining the different data sets works if I don't give anything for the 'arrayNames' 
parameter in readIllumina() but then  all the files in the directory are read.

This small data set is only for testing and in the future I would like to combine many 
chips into one object, not necessarily including every sample on each array.

Thanks in advance,
Asta

Below is the code and session information.

---

library(beadarray)

data <- readIllumina(path="1735640017",
                     textType=".txt",
                     arrayNames=c("1735640017_A_1", "1735640017_A_2",
                                  "1735640017_D_1", "1735640017_D_2")
                     )

Found 4 arrays
Reading pixels of 1735640017/1735640017_A_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_D_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_D_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract


data <- createBeadSummaryData(data, imagesPerArray = 2)

exprs(data)[1:10,]

     1735640017_A_1 1735640017_D_1
10243      148.28308       157.3592
10280       96.39223       108.3309
10575      132.72321       136.9459
20048      106.45987       125.9253
20296    12385.10467     11879.6216
20343      470.61351       293.3878
20373      114.44354       133.7846
20431    25695.85350     30478.6505
50008      607.38792       631.1659
50014       86.33236        89.1350



data2 <- readIllumina(path="1735640018",
                      textType=".txt",
                      arrayNames=c("1735640018_A_1", "1735640018_A_2",
                                   "1735640018_D_1", "1735640018_D_2")
                     )
Found 4 arrays
arrayNames(dataReading pixels of 1735640018/1735640018_A_1_Grn.tif
2)
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_D_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_D_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract


data2 <-  createBeadSummaryData(data2, imagesPerArray = 2)


exprs(data2)[1:10,]

      1735640018_A_1 1735640018_D_1
10243       147.6654      153.04544
10280       113.3786      101.17059
10575       130.5891      123.23560
20048       113.0089      114.82174
20296     12992.2415     9307.39043
20343       336.2219      415.96840
20373       110.7654      115.41545
20431     27717.1189    16975.48752
50008       550.6863      542.58111
50014        92.1901       80.69506


combinedData <- combine(data, data2)
Error in combine(pDataX, pDataY) : data.frames contain conflicting data:
        non-conforming colname(s): arrayName
    

#---------------------------------------------------------------------------
> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;
LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
  beadarray        affy      affyio geneplotter     lattice    annotate
   "1.5.14"    "1.14.0"     "1.4.0"    "1.14.0"    "0.15-4"    "1.14.1"
    Biobase       limma
   "1.14.0"    "2.10.0"