[BioC] Questions about calculate gene signal

[Richard Friedman]

Dear Yang,

	The easiest way I know if you are starting out is the AffylmGUI and  
oneChannelGUI programs.,
oneChannelGUI is the more powerful of the two., but AffylmGUI has more  
detailed on line turoials
with test cases. Working through teh worked examples will answer your  
questions.

	I can also send you my course material off-line on the theory if it  
will help.

Best wishes,
Rich

On Jun 17, 2010, at 10:13 AM, Yang Lv wrote:

> Dear Richard,
>
> It's Affymetrix.
>
> On Thu, Jun 17, 2010 at 9:16 PM, Richard Friedman <friedman at cancercenter.columbia.edu 
> > wrote:
> Dear Yang,
>
>        What kind of array are you using (Affymetrix, 2 color etc)?
>
> Best wishes,
> Rich
> ------------------------------------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In Memoriam,
> George Scithers
>
>
>
>
> On Jun 17, 2010, at 12:22 AM, Yang Lv wrote:
>
> Dear List,
>
> I'm new to microarray analysis and need to calculate gene signal from
> samples. The tab-delimited file has been prepared and the signal for  
> each
> probe is calculated. My question is: 1) How to filter the probes  
> those are
> disqualified? 2) How to calculate the gene signal from probe signal?  
> The
> reflection from probes to genes are clear but I have no idea if I  
> need to
> simply sum up all the probes of a given gene or something else.
>
> Thanks a lot and best wishes.
>
> -- 
> Lv Yang
>
> School of Life Sciences
> Sun Yat-Sen University
> Guangzhou, 510275, Guangdong
> P. R. China
>
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>
>
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>
>
>
> -- 
> Lv Yang
>
> School of Life Sciences
> Sun Yat-Sen University
> Guangzhou, 510275, Guangdong
> P. R. China