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

[Steve Lianoglou]

Hi Tao,

I was curious if you took an approach in your analysis that borrowed  
from the BioC `tilingArray` package, or is your take something  
completely new/different?

I'm playing around with analyzing some tiling array data myself for  
the first time, and was curious how you approached some issues in the  
analysis, such as:

1) normalization of signal with respect to probe sequence
--> The process outlined in the tilingArray package for dealing with  
this sounds great, but I don't have genomic dna to use as a control.

2) dealing with probes that hit several parts of the genome

3) did you reblast the probe sequences to get a better idea of where  
they map to the latest reference genome?

Just curious,
-steve


On May 8, 2008, at 6:01 PM, Shi, Tao wrote:

> 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.
>
> ...Tao
>
>
>
>
> ----- 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.
>
> Kasper
>
> 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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