[BioC] beadarray - combing

Krys Kelly kak28 at cam.ac.uk
Wed Aug 8 18:07:52 CEST 2007


I have been using beadarray to explore 5 Illumina mouse 6 bead chips (i.e.
30 arrays).  I would now like to summarise the data using
createBeadSummaryData.  As the documentation says, this is memory intensive
and I do not believe it will be possible to do with with a 32-bit version of
R.  I am looking into the possibility of being able to use a 64-bit
compilation.  However, this may take some time.

So I was attracted by the help for this function which says: 

" Objects which are created separately by 'createBeadSummaryData' may be
joined by using the cbind function. "

I don't know what the trick is, but this doesn't work for me.  I just wind
up with a 1x2 matrix containing the names of the two bead summary objects I
am trying to combine.

Here is my code and session information.

Thanks for any help.

Cheers

Krys


> BLData39ABC <- readIllumina(arrayNames=c(
+                             "1863191039_A_1", "1863191039_A_2",
+                             "1863191039_B_1", "1863191039_B_2",
+                             "1863191039_C_1", "1863191039_C_2"),
+                           textType=".txt",
+                           backgroundMethod="none", normalizeMethod="none")
Found 6 arrays 
Reading pixels of 1863191039_A_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_B_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_B_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_C_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_C_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 

> BLData39DEF <- readIllumina(arrayNames=c(
+                             "1863191039_D_1", "1863191039_D_2",
+                             "1863191039_E_1", "1863191039_E_2",
+                             "1863191039_F_1", "1863191039_F_2"),
+                           textType=".txt",
+                           backgroundMethod="none", normalizeMethod="none")
Found 6 arrays 
Reading pixels of 1863191039_D_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_D_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_E_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_E_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_F_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
Reading pixels of 1863191039_F_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = none 
> 
> # Creation of summary data
> cat("\nCreating summary data\n")

Creating summary data
> flush.console()
NULL
> BSData39ABC
<-createBeadSummaryData(BLData39ABC,log=FALSE,n=3,imagesPerArray=2)
> BSData39DEF
<-createBeadSummaryData(BLData39DEF,log=FALSE,n=3,imagesPerArray=2)
> 
> exprs(BSData39ABC)[1:10, 1:3]
      1863191039_A_1 1863191039_B_1 1863191039_C_1
10243       839.6506       845.9098       865.9043
10280       833.1207       834.3494       848.4542
10575       904.3008       910.9755       944.9005
20048       829.4193       827.7526       842.6774
20296     19276.8925     21378.0448     23450.6285
20343       815.6845       817.2897       833.3593
20373       820.7240       820.3355       833.8266
20431     27753.5007     29888.2093     29346.2453
50008       869.3557      1024.7717      1022.3103
50014       800.8334       799.2665       809.7410
> exprs(BSData39DEF)[1:10, 1:3]
      1863191039_D_1 1863191039_E_1 1863191039_F_1
10243       839.3879       861.5757       854.2918
10280       831.0985       838.2159       858.3772
10575       896.9414       910.2924       925.6573
20048       833.0732       835.5710       844.9445
20296     21587.3530     19046.5401     22171.7225
20343       833.2653       829.7436       835.0217
20373       828.0081       835.3683       842.4046
20431     32288.4499     28639.5432     31756.6553
50008      1059.4472      1019.7494      1020.6142
50014       807.6089       802.2027       812.7708
> 
> BSData <- cbind(BSData39ABC, BSData39DEF)
> 
> exprs(BSData)[1:10, 1:3]
Error in function (classes, fdef, mtable)  : 
        unable to find an inherited method for function "exprs", for
signature "matrix"
> 
> BSData
     BSData39ABC BSData39DEF
[1,] ?           ?
          
> class(BSData)
[1] "matrix"

> attributes(BSData)
$dim
[1] 1 2

$dimnames
$dimnames[[1]]
NULL

$dimnames[[2]]
[1] "BSData39ABC" "BSData39DEF"


> sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.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"       "4.08"
"0.73" 
        affy       affyio  geneplotter      lattice     annotate
Biobase 
    "1.14.2"      "1.4.1"     "1.14.0"    "0.15-11"     "1.14.1"
"1.14.1" 
       limma 
    "2.10.5" 
>



Dr Krystyna A Kelly (Krys)
 
Department of Pathology
University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
Tel: 01223 333331

and

MRC Biostatistics Unit
Institute of Public Health, Robinson Way, Cambridge CB2 0SR
Tel: 01223 767408

Email: kak28 at cam.ac.uk



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