[BioC] boxplots using beadarray

[Mark Dunning]

Hi,

Thanks for the report. I noticed the bug and thought it should have
been fixed in beadarray 2.0.1. The only the thing I can suggest is try
to update again (latest version is 2.0.2) and see if the bug still
appears.

Regards,

Mark

On Wed, Nov 3, 2010 at 9:21 PM, Ying W <daiyingw at gmail.com> wrote:
> Hi,
> I've been trying to follow some of the QC steps listed on "Analysis of
> Bead-level Data using beadarray" (dated October 23, 2010)
> Seems like BLData variable is hardcoded:
>
>>library(beadarray)
>>ar1 = readIllumina(dir = "4849554032", useImages = FALSE,
> illuminaAnnotation = "Humanv3", metricsFile = "Metrics.txt")
> .....
>> boxplot(ar1, las = 2, outline = FALSE, ylim = c(4,12), main = "Green
> Foreground")
> Error in getBeadData(BLData, array = array, what = "Grn") :
>  object 'BLData' not found
>> boxplot(BLData=ar1, las = 2, outline = FALSE, ylim = c(4,12), main =
> "Green Foreground")
> Error in list(x, ...) : 'x' is missing
>> BLData = ar1
>> boxplot(BLData) #this works
>
> Thanks,
> Ying Wu
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i486-pc-linux-gnu (32-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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] beadarray_2.0.1 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.4  tcltk_2.12.0 tools_2.12.0
>
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