[BioC] Help for readIllumina beadlevel error

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Sun Mar 2 20:20:02 CET 2008

Thank you. The chips used for my experiment were the RatRef-12
expression beadchips. 

-----Original Message-----
From: Matt Ritchie [mailto:Matt.Ritchie at cancer.org.uk] 
Sent: Saturday, 1 March 2008 3:36 a.m.
To: Johnstone, Alice
Cc: bioconductor
Subject: Re: [BioC] Help for readIllumina beadlevel error

Hi Alice,

Thanks for your email.  This is a bug, which should be fixed in
beadarray 1.7.4.  Most arrays we see (those from SAMs and WG6 chips) are
named using the convention chipID_row_column, and this information is
stored along with other processing options in the arrayInfo slot of a
BeadLevelList.  Your arrays look to be named as chipID_row, and when
readIllumina() attempts to store something for column, you get the error
below.  I guess this naming convention is used for human/mouse 8 arrays?

Best wishes,


> Hi
> I want to read in each array at beadlevel separately, but when I do 
> this I get the following error:
> B13Data<-readIllumina(arrayNames=c("4194720030_F"),textType=".txt",bac
> kg
> roundMethod
> +
> ="none",offset=0,normalizeMethod="none",metrics=FALSE,useImages=TRUE,t
> ar
> gets=targets)
> Found 1 arrays
> Error in seq.default(3, length(tmp), by = 3) :
>   wrong sign in 'by' argument
>> sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New 
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> [8] base     
> other attached packages:
>  [1] illuminaRatBCv1_1.1.0 beadarray_1.6.0       affy_1.16.0
>  [4] preprocessCore_1.0.0  affyio_1.6.1          geneplotter_1.16.0
>  [7] lattice_0.17-4        annotate_1.16.1       xtable_1.5-2
> [10] AnnotationDbi_1.0.6   RSQLite_0.6-7         DBI_0.2-4
> [13] Biobase_1.16.3        limma_2.12.0
> loaded via a namespace (and not attached):
> [1] grid_2.6.2         KernSmooth_2.22-22 RColorBrewer_1.0-2
> Can someone explain what I've done wrong?
> Thanks!
> Alice Johnstone

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