[BioC] beadarray - combing
Mark Dunning
md392 at cam.ac.uk
Thu Aug 9 01:21:12 CEST 2007
Hi Krys,
Sorry, it seems that the manual page for createBeadSummaryData is
either out of date or contains a typo. The function we use to join
summarised data is actually called combine
so you would use
BSData = combine(BSData39ABC, BSData39DEF)
to get the required result.
Hope this helps and thanks for bringing it to my attention
Regards,
Mark
On 8 Aug 2007, at 17:07, Krys Kelly wrote:
> 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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