[BioC] beadarray package question

Mark Dunning Mark.Dunning at cancer.org.uk
Fri Nov 14 16:08:32 CET 2008


Thanks for your questions. The first relates to a new piece of
functionality added to beadarray that has not been explained in depth

1. The names Humanv3, Humanv2, Humanv1 etc are used to identify the type
of chip being read in. This is so we know the ids of the control probes
on the chip (which change between versions and organisms). The
information about the control probes is stored with the package so there
is no need to download extra information. It is completely separate to
the annotation Illumina provides and the Bioconductor packages. The
naming convention we used is chosen to match the names of the annotation
packages available from Bioconductor. For example if you have a
HumanWG-6 v3 Expression array you would specify annoPkg="Humanv3" when
you load data with readIllumina and then use the
illuminaHumanv3BeadID.db annotation package later on.

2. Can you list the files that are in the working directory where you
are trying to read from? Each sample should have a _Grn.tif and .txt
file for a bead-level analysis



PS posting the result of running the command sessionInfo() is also
useful so we know what version of packages you are running.

On Thu, 2008-11-13 at 21:02 -0500, Fu Sheng wrote:
> Hello, there,
> I am using beadarray package developed by Mark Dunning for Illumina
> expression arrays. Have 2 question regarding to this package:
> 1. There is annotation file Illumina_HumanWG-6_V2_0_R1_11223189_A.bgx in the
> data set I downloaded form GEO. Unfortunately readIllumina() didn't
> recognize this file, instead it asked for "Humanv3 Humanv2 Humanv1
> Mousev2 Mousev1 Mousev1p1 Ratv1". Illumina has expression arrays:
> - HumanHT-12 Expression BeadChip
> - HumanWG-6 v3 Expression
> - HumanRef-8 v3 Expression BeadChip
> - MouseWG-6 v2 Expression
> - MouseRef-8 v2 Expression BeadChip
> - RatRef-12 Expression BeadChip
> So where I can get these "Humanvs, Humanv2..." files? and which annotation
> is for which array?
> 2. There are tif files for each sample in data set. But file extension is
> .tif not_Grn.tif. I got following errors when reading data. What's wrong?
> ------------------------------------------------------------------------------------------------------------------------
> > d<-readIllumina(useImages=T, tiffExtGrn=".tif")
> Found 0 arrays
> Error in seq.default(1, length(tmp), by = 3) :
> wrong sign in 'by' argument
> In addition: Warning message:
> In readIllumina(useImages = T, tiffExtGrn = ".tif") :
> No annotation package was specified. Need to use SetAnnotation later
> -------------------------------------------------------------------------------------------------------------------------
> Thank you very much.
> yezhou
> 	[[alternative HTML version deleted]]
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