[BioC] Analysis for only 2 replicates

[Khan, Sohail]

Thanks everyone for your advice.  I have decided to use Limma, however I am not sure how to set up the design matrix for this analysis. Thanks again for your help..

-Sohail

-----Original Message-----
From: fhong at salk.edu [mailto:fhong at salk.edu]
Sent: Wednesday, March 08, 2006 7:35 PM
To: Sean Davis
Cc: Khan, Sohail; Bioconductor
Subject: Re: [BioC] Analysis for only 2 replicates


Based on my experience,SAM usually fails with only 2 replicates under each
condition.
Limma and RankProd both can handle 2 replicates.

Fangxin

>
>
>
> On 3/8/06 4:07 PM, "Khan, Sohail" <khan at cshl.edu> wrote:
>
>> Dear list,
>>
>> I have 2 -wt and 2-mutant samples done on Affymetrix chips.
>> Could you suggest the best way to analyze this experiment? Is averaging
>> both
>> replicates and picking genes based on fold change good??
>> Thanks for any suggestions.
>
> I wouldn't average if you can help it (if these are biological
> replictes--if
> they are not, then I would argue that you don't actually have any
> replication).  You are then very much at the mercy of the outliers.  I
> would
> try using limma or SAM, or one of several other methods for looking at
> microarray data designed with small samples in mind.
>
> That said, any results that you find are very suspect with only two
> replicates per condition, but if you are only interested in finding
> candidates for further analysis (the best you can hope to do with only
> four
> arrays), the ordering you get would, I think, be more robust using a
> statistical test than simple averaging.
>
> Sean
>
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>


--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105