[BioC] Help for readIllumina beadlevel error
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
From: Matt Ritchie [mailto:Matt.Ritchie at cancer.org.uk]
Sent: Saturday, 1 March 2008 3:36 a.m.
To: Johnstone, Alice
Subject: Re: [BioC] Help for readIllumina beadlevel error
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?
> I want to read in each array at beadlevel separately, but when I do
> this I get the following error:
> Found 1 arrays
> Error in seq.default(3, length(tmp), by = 3) :
> wrong sign in 'by' argument
> R version 2.6.2 (2008-02-08)
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
> attached base packages:
>  tools stats graphics grDevices utils datasets
>  base
> other attached packages:
>  illuminaRatBCv1_1.1.0 beadarray_1.6.0 affy_1.16.0
>  preprocessCore_1.0.0 affyio_1.6.1 geneplotter_1.16.0
>  lattice_0.17-4 annotate_1.16.1 xtable_1.5-2
>  AnnotationDbi_1.0.6 RSQLite_0.6-7 DBI_0.2-4
>  Biobase_1.16.3 limma_2.12.0
> loaded via a namespace (and not attached):
>  grid_2.6.2 KernSmooth_2.22-22 RColorBrewer_1.0-2
> Can someone explain what I've done wrong?
> Alice Johnstone
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