[BioC] some basic questions

Richard Friedman friedman at cancercenter.columbia.edu
Wed Nov 30 15:43:15 CET 2011

Dear Anand,


On Nov 30, 2011, at 2:04 AM, anand mt [guest] wrote:

> Hi all..
> i have following questions.
> 1) How many probesets represent a gene on microarray chip ?

See manufactures literature for chip.

> 2) How do i access raw intesity value of probes (before  
> normalization) ?
> 3) Do i need to read cdf file to do that ??

2 & 3. Follow the worked examples with affylmGUI,

> 4) After pre-processing the data and normalization, we generally go  
> for significance tests and gene grouping. My question is, if i group  
> the genes before performing  significance test (say now i have 3  
> groups based on apoptosis,cell cycle, DNA replication) and then  
> perform significance test within each group, will the results be  
> same as that of conventional way ?? Is it a valid method to do so??

I don't understand this question, but get a list of differentially  
expressed genes first,
The onto-express and pathway-express web sites for which I sent you  
the  links in
the course handouts I sent you should enable you to do a good post- 
gene list analysis.

Best wishes,

> Sorry if my questions are silly.
> -- output of sessionInfo(): 
> --NONE--
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Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
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

I am a Bayesian. When I see a multiple-choice question on a test and I  
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14

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