[BioC] combineBeadLevelLists() in Bioconductor 2.8 beadarray

[Alex Gutteridge]

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