[BioC] Affymetrix data

[Edwin Groot]

On Fri, 13 Apr 2012 16:09:39 +0000
 <hsharm03 at students.poly.edu> wrote:
> 
> Dear all,
> This question might sound very naive to most of you but I am new at
> analyzing affymetrix array data using R/Bioconductor packages. 
> I have two cel files generated from HT430 Mouse genome. I have to
> find differentially expressed genes in the treated mouse as compared
> to the control.
> For this , I downloaded the "affy" package and got the express set
> (eset) of the differentially expressed genes. I used the rma function
> to normalization , Background correction and differential expression.
> Now , I want to annotate these genes and find out there significance
> in several Pathways. How do I go about doing that?. Also , I read a
> few topics where they say I need to load the library of annotation
> (ht430mg here). But where do I get this database?. 
> Any help will be much appreciated as I am new to this topic any sort
> of guidance will be really helpful.
> Thanks,
> Himanshu Sharma. 		 	   		  

Hello Himanshu,
Check out the workflows at the Bioconductor Web site. Read the manuals
of the packages. Run the sample sessions.
http://bioconductor.org/help/workflows/

In your case, clicking the Accessing Annotation Data link would help.

Regards,
Edwin
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Dr. Edwin Groot
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032948