[BioC] General question about library files

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Aug 18 18:01:45 CEST 2008

Hi John,

As the previous two replies from James and Henrik seem to have  
addressed most of your questions, I'll just go to the one that wasn't:

On Aug 15, 2008, at 4:12 PM, John O. Woods wrote:
> I've been looking for a good resource to help me get a handle on this
> stuff. I see lots of tutorials and stuff for analyzing microarrays,
> but little for tiling arrays (yay cutting edge). Anyone have any
> pointers?

The thing about tiling arrays is that there aren't that many tutorials  
readily available for you to apply out of the box.

You didn't mention what you are using the tiling array for. I'll  
assume you're using it for something like transcript mapping, just  
because that's what I was trying to do. If you're using it for ChIP- 
chip, the Ringo and oligo packages (I've been told) are a good place  
to start.

(1) the BioC::tillingArray and BioC:davidTiling packages could be a  
good place to start:


You'll most likely find it hard to directly apply the tilingArray  
package to your problem at hand, so the publications that describe the  
technique are also quite helpful to get you moving in the right  

Transcript mapping with high-density oligonucleotide tiling arrays
22/16/1963 [method]

A high-resolution map of transcription in the yeast genome
http://www.pnas.org/content/103/14/5320.abstract [application]

It's definitely a good read to start with. One issue is that their  
normalization method requires experiments that use genomic DNA  
hybridized to the chip. Since this isn't "standard," it's quite likely  
(and unfortunate) that you won't be able to use it. Still, you should  
read it :-) If you can't use their normalization, you may still be  
able to use the tilingArray package for its segmentation algorithm.

(2) If you can't go with (1), you can look at:

At-TAX: a whole genome tiling array resource for developmental  
expression analysis and transcript identification in Arabidopsis  
thaliana [application/method]

Transcript Normalization and Segmentation of Tiling Array Data

The latter is a thorough write-up of the technique used in the former.  
Their normalization code is made available through the second link as  
well. It is written in MATLAB, however. In order to use it, you will  
have to annotate your probe-data and shoe-horn it into their pipeline  
w/ the appropriate tiling array data.

Hope that helps,

Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University


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