[BioC] combineBeadLevelLists() in Bioconductor 2.8 beadarray

[Mark Dunning]

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
>>>
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>
> --
> Alex Gutteridge
>