[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either out of date or contains a typo.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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