Hi Karthik,

Since you have two groups, if could use a simple t-test and correct the p-values for multiple testing using Benjamin-hochberg. Besides the t-test, I would suggest to you the sam.r package to find the differentially expressed genes.  
I have never use BGX with agilent, so I am not sure that this would work.

Let me know if you need further help.

Best,
Lucas


On Feb 6, 2012, at 8:29 AM, Karthik K N wrote:

> Dear Lucas,
> 
> I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits.
> 
> I read your posts and the replies to that. 
> 
> My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them. 
> 
> From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets?
> 
> I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not. 
> 
> If there is there anything that you can do to help me solve this, I will be really thankful to you. 
> 
> 
> Thank you
> 
> Karthik.
> -- 
> Karthik K.N
> 
> 


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