[BioC] create Affymetrix .chp file for viewing in affy Integrated Genome Browser
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Fri May 9 19:40:06 CEST 2008
I was curious if you took an approach in your analysis that borrowed
from the BioC `tilingArray` package, or is your take something
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?
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.
> ----- 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
>> corresponding chormosomal coordinates). Are there ways to package
>> 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
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