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<http: www.illumina.com="" pages.ilmn?id="282"> - HumanWG-6 v3 Expression BeadChip<http: www.illumina.com="" pages.ilmn?id="197"> - HumanRef-8 v3 Expression BeadChip <http: www.illumina.com="" pages.ilmn?id="197"> - MouseWG-6 v2 Expression BeadChip<http: www.illumina.com="" pages.ilmn?id="198"> - MouseRef-8 v2 Expression BeadChip <http: www.illumina.com="" pages.ilmn?id="198"> - RatRef-12 Expression BeadChip <http: www.illumina.com="" pages.ilmn?id="199"> 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]]