Search
Question: beadarray question
0
gravatar for Fu Sheng
8.5 years ago by
Fu Sheng30
Fu Sheng30 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<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]]
ADD COMMENTlink written 8.5 years ago by Fu Sheng30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 225 users visited in the last hour