[BioC] makePDpackage for tiling arrays

[Jenny Drnevich]

Hi Benilton & all,

I've gotten some data from Affy's mouse promoter 1.0R tiling array, and I'm 
trying to figure out how to analyze it. I've looked in the archives, and 
found some of your posts about the oligo and makePlatformDesign packages 
very helpful:

https://stat.ethz.ch/pipermail/bioconductor/2007-January/015655.html
https://stat.ethz.ch/pipermail/bioconductor/2006-August/014167.html

My question: what's the meaning of the different arguments for 
makePDpackage? In your tutorial slides from BioC2006, you show it called 
along these lines:

makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", genomebuild="mg33")

However, in the August post above, it was being used this way:

makePDpackage("Hs_PromPF_v02-3_NCBIv34.bpmap",  file1="Hs_PromPF_v02.cif", 
manufacturer="affymetrix", type="tiling")


What is the file1 argument? The help page doesn't say what these should be 
for tiling arrays, and it appears from your tutorial that it's not 
necessary. For the mouse promoter tiling array, there are two .cif files, 
one forward and one reverse. Here's what Affy's readme file said about 
them: "The R and F tiling sets have been split into two separate zip files 
so make sure you have the right file."

Should I be using these? How should I be using these? My first goal is just 
to look at the raw data values, and there are only 2 arrays - one CHip and 
one control. The researchers want see how well these arrays turned out, and 
get some idea on what level of replication may be needed. And if anyone 
knows any good articles on analyzing CHip-on-chip arrays, please point them 
out to me - I've been finding some, but I would like to know what others 
have found useful.

Thanks,
Jenny


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu