[BioC] combineBeadLevelLists() in Bioconductor 2.8 beadarray
Alex Gutteridge
alexg at ruggedtextile.com
Tue Dec 7 14:51:21 CET 2010
Everything looks OK - I see the beadLevelData combine() method. Can you
see anything obviously wrong with the beadLevelData objects themselves? The
only thing that I can see is that the Metrics are all NA.
> class(iBatch1)
[1] "beadLevelData"
attr(,"package")
[1] "beadarray"
> class(iBatch2)
[1] "beadLevelData"
attr(,"package")
[1] "beadarray"
> showMethods("combine")
Function: combine (package Biobase)
x="AnnotatedDataFrame", y="AnnotatedDataFrame"
x="ANY", y="missing"
x="AssayData", y="AssayData"
x="beadLevelData", y="beadLevelData"
x="data.frame", y="data.frame"
x="eSet", y="eSet"
x="ExpressionSetIllumina", y="ExpressionSetIllumina"
x="ExpressionSet", y="LumiBatch"
x="LumiBatch", y="ExpressionSet"
x="LumiBatch", y="LumiBatch"
x="matrix", y="matrix"
x="MethyLumiSet", y="MethyLumiSet"
x="MIAME", y="MIAME"
> iBatch1
Experiment information
$sdfFile
[1] "/data1/Projects/Pancreas/inVivo/5168671015/5168671015.sdf"
$platformClass
[1] "Slide"
$annotation
[1] "Humanv4"
Targets
directory sectionName
textFile
1 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_A_1
5168671015_A_1.txt
2 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_B_1
5168671015_B_1.txt
3 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_C_1
5168671015_C_1.txt
4 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_D_1
5168671015_D_1.txt
5 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_E_1
5168671015_E_1.txt
greenImage
1 5168671015_A_1_Grn.tif
2 5168671015_B_1_Grn.tif
3 5168671015_C_1_Grn.tif
4 5168671015_D_1_Grn.tif
5 5168671015_E_1_Grn.tif
.. 2 more columns of data
Metrics
Date Beadchip Section FocusGrn
NA <NA> NA <NA> NA
NA.1 <NA> NA <NA> NA
NA.2 <NA> NA <NA> NA
NA.3 <NA> NA <NA> NA
NA.4 <NA> NA <NA> NA
.. 7 more columns of data
SampleGroup
[1] A B C D E
Levels: A B C D E F G H I J K L
numBeads
[1] 1018509 1014208 1029054 1015868 1016981
Array information
Raw data from section 5168671015_A_1
ProbeID GrnX GrnY Grn
[1,] 10008 1640.5000 24330.480 1021
[2,] 10008 302.5283 24325.500 613
[3,] 10008 540.5187 19041.480 640
[4,] 10008 1219.5060 1755.484 968
[5,] 10008 1031.5120 20808.510 1217
... 1018504 more rows of data
... data for 11 more array/s
> iBatch2
Experiment information
$sdfFile
[1] "/data1/Projects/Pancreas/inVivo/5168671022/5168671022.sdf"
$platformClass
[1] "Slide"
$annotation
[1] "Humanv4"
Targets
directory sectionName
textFile
1 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_A_1
5168671022_A_1.txt
2 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_B_1
5168671022_B_1.txt
3 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_C_1
5168671022_C_1.txt
4 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_D_1
5168671022_D_1.txt
5 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_E_1
5168671022_E_1.txt
greenImage
1 5168671022_A_1_Grn.tif
2 5168671022_B_1_Grn.tif
3 5168671022_C_1_Grn.tif
4 5168671022_D_1_Grn.tif
5 5168671022_E_1_Grn.tif
.. 2 more columns of data
Metrics
Date Beadchip Section FocusGrn
NA <NA> NA <NA> NA
NA.1 <NA> NA <NA> NA
NA.2 <NA> NA <NA> NA
NA.3 <NA> NA <NA> NA
NA.4 <NA> NA <NA> NA
.. 7 more columns of data
SampleGroup
[1] A B C D E
Levels: A B C D E F G H I J K L
numBeads
[1] 1042066 1036063 1050477 1047443 1054511
Array information
Raw data from section 5168671022_A_1
ProbeID GrnX GrnY Grn
[1,] 10008 1703.4920 658.5403 1029
[2,] 10008 1103.4780 8908.4650 650
[3,] 10008 1938.5220 14068.5000 699
[4,] 10008 1781.4860 6699.4960 904
[5,] 10008 798.4817 1983.4770 1242
... 1042061 more rows of data
... data for 11 more array/s
On Tue, 7 Dec 2010 13:14:57 +0000, Mark Dunning <mark.dunning at gmail.com>
wrote:
> Hi Alex,
>
> No, you're correct. That should be how to combine two object and it's
> not immediately clear what the problem might be. If you run
>
>>showMethods("combine")
>
> Do you see a method listed that combines beadLevelData objects? Do
> iBatch1 and iBatch2 look like valid beadLevelData objects?
>
>>iBatch1
>>iBatch2
>
> Mark
>
> On Tue, Dec 7, 2010 at 11:32 AM, Alex Gutteridge
> <alexg at ruggedtextile.com> wrote:
>> Hi Mark,
>>
>> Sorry, maybe I'm being dim, but how do you call combine() correctly?
>>
>>> dir1 <- "/5168671015"
>>> iBatch1 <- readIllumina(dir = paste(".", dir1, sep = ""),
>> + useImages = FALSE,
>> + metricsFile = "Metrics.txt",
>> + illuminaAnnotation="Humanv4")
>> Processing section 5168671015_A_1
>> Processing section 5168671015_B_1
>> Processing section 5168671015_C_1
>> Processing section 5168671015_D_1
>> Processing section 5168671015_E_1
>> Processing section 5168671015_F_1
>> Processing section 5168671015_G_1
>> Processing section 5168671015_H_1
>> Processing section 5168671015_I_1
>> Processing section 5168671015_J_1
>> Processing section 5168671015_K_1
>> Processing section 5168671015_L_1
>>> dir2 <- "/5168671022"
>>> iBatch2 <- readIllumina(dir = paste(".", dir2, sep = ""),
>> + useImages = FALSE,
>> + metricsFile = "Metrics.txt",
>> + illuminaAnnotation="Humanv4")
>> Processing section 5168671022_A_1
>> Processing section 5168671022_B_1
>> Processing section 5168671022_C_1
>> Processing section 5168671022_D_1
>> Processing section 5168671022_E_1
>> Processing section 5168671022_F_1
>> Processing section 5168671022_G_1
>> Processing section 5168671022_H_1
>> Processing section 5168671022_I_1
>> Processing section 5168671022_J_1
>> Processing section 5168671022_K_1
>> Processing section 5168671022_L_1
>>> iBatch = combine(iBatch1,iBatch2)
>> Error in combine(iBatch1, iBatch2) : unable to combine these objects
>>> class(iBatch1)
>> [1] "beadLevelData"
>> attr(,"package")
>> [1] "beadarray"
>>> class(iBatch2)
>> [1] "beadLevelData"
>> attr(,"package")
>> [1] "beadarray"
>>
>> On Tue, 7 Dec 2010 10:46:21 +0000, Mark Dunning
<mark.dunning at gmail.com>
>> wrote:
>>> Hi Alex,
>>>
>>> The functionality still exists in beadarray, but can be called using
>>> the generic 'combine' rather than combineBeadLevelLists.
>>>
>>> Best wishes,
>>>
>>> Mark
>>>
>>> On Tue, Dec 7, 2010 at 10:20 AM, Alex Gutteridge
>>> <alexg at ruggedtextile.com> wrote:
>>>> Hi,
>>>>
>>>> Older versions of beadarray have a combineBeadLevelList() for
combining
>>>> bead level data lists read from two different Illumina chips into one
>>>> list.
>>>> In the latest beadarray this seems to have been removed, but I can't
>> find
>>>> anything in the documentation describing the correct way to do this
>> with
>>>> the new beadLevelData class. Am I missing something obvious or is
this
>> no
>>>> longer supported?
>>>>
>>>>> sessionInfo()
>>>> R version 2.12.0 (2010-10-15)
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] splines stats graphics grDevices utils datasets
>>>> methods
>>>> [8] base
>>>>
>>>> other attached packages:
>>>> [1] reshape_0.8.3 plyr_1.2.1 nlme_3.1-97
>>>> [4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 RSQLite_0.9-3
>>>> [7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.0
>>>> [10] limma_3.6.6 latticeExtra_0.6-14 RColorBrewer_1.0-2
>>>> [13] lattice_0.19-13 contrast_0.13 Design_2.3-0
>>>> [16] Hmisc_3.8-3 survival_2.36-1 Cairo_1.4-5
>>>> [19] beadarray_2.0.2 Biobase_2.10.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0
>>>> [4] cluster_1.13.2 grid_2.12.0 hdrcde_2.14
>>>> [7] KernSmooth_2.23-4 MASS_7.3-8 Matrix_0.999375-44
>>>> [10] methylumi_1.4.0 mgcv_1.7-1
preprocessCore_1.12.0
>>>> [13] tcltk_2.12.0 tools_2.12.0 xtable_1.5-6
>>>>
>>>> --
>>>> Alex Gutteridge
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>
>> --
>> Alex Gutteridge
>>
--
Alex Gutteridge
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