[BioC] Regarding merging technical spot replicates in microarray data for analysis

[Steve Lianoglou]

Hi Ankhee,

On Aug 6, 2009, at 1:01 AM, ankhee dutta wrote:

> Hi all,
> I am having problem in merging technical spot replicates in  
> microarray data
> for further analysis of it. I want to get rid of outliers so i dont  
> want to
> just average them. I have microarray datasets from different  
> experiments
> with their log2 based ratio values and nothing else so how can i  
> detect the
> outliers.
> I tried to use tools like GEPAS but it was just averaging the  
> replicate
> values.So please suggest some tools or ways to do this.
> Please help me out.
> Thank you in advance.Any relevant answer will be appreciated.

Sorry, it's not clear to me if you're talking about summarizing  
replicate spots on one array, or across arrays -- either way, I  
believe the limma package should be able to help you out here. The  
package comes with a rather extensive user guide that wouldn't hurt to  
read through as it covers many aspects of dealing with microarray data  
in R.

As an example, here's an older version of the doc which mentions  
duplicate spots on an array:

http://pbil.univ-lyon1.fr/library/limma/doc/usersguide.html#DuplicateSpots

Hope that helps,

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact