[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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