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

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