[BioC] create Affymetrix .chp file for viewing in affy Integrated Genome Browser

Shi, Tao shidaxia at yahoo.com
Fri May 9 00:01:59 CEST 2008

Hi Kasper,

Thanks for the reply!

Actually, I just found out that .sgr format, which is just a simple text with columns of coordinate and score, will do.

Thanks a lot.


----- Original Message ----
From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
To: "Shi, Tao" <shidaxia at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Sent: Thursday, May 8, 2008 12:28:19 PM
Subject: Re: [BioC] create Affymetrix .chp file for viewing in affy Integrated Genome Browser

There are two my mind no facilities for this. The natural place for  
such functions would be affxparser (which I maintain) and right now we  
have no plans for such an addition).

But IGB supports many different formats, most of which are super easy  
to write using write.table. For examples BED files (I think they are  
called). Look in the IGB manual for further info. There might even be  
a package that does this for you.


On May 8, 2008, at 10:47 AM, Shi, Tao wrote:

> Hi list,
> I have my customized analysis
> results of a tiling array data set (signal changes, p values, and  
> their
> corresponding chormosomal coordinates). Are there ways to package them
> into Affy .chp files so I can to view them in IGB?  Or if you know  
> any other applications that function like IGB, please also let me  
> know.
> Thanks,
> ...Tao
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